data_17453
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data
;
_BMRB_accession_number 17453
_BMRB_flat_file_name bmr17453.str
_Entry_type original
_Submission_date 2011-02-09
_Accession_date 2011-02-09
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details 'Tetrameric model of the inflammatory chemokine CCL5/RANTES'
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Wang Xu . .
2 Watson Caroline M. .
3 Sharp Joshua S. .
4 Handel Tracy M. .
5 Prestegard James H. .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 58
"15N chemical shifts" 59
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2011-08-17 original BMRB .
stop_
_Original_release_date 2011-02-18
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data.
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 21827949
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Wang Xu . .
2 Watson Caroline . .
3 Sharp Joshua S. .
4 Handel Tracy M. .
5 Prestegard James H. .
stop_
_Journal_abbreviation Structure
_Journal_name_full 'Structure (London, England : 1993)'
_Journal_volume 19
_Journal_issue 8
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 1138
_Page_last 1148
_Year 2011
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name ccl5
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
chain_1 $ccl5
chain_2 $ccl5
chain_3 $ccl5
chain_4 $ccl5
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state ?
_System_paramagnetic no
_System_thiol_state .
_Database_query_date .
_Details .
save_
########################
# Monomeric polymers #
########################
save_ccl5
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common ccl5
_Molecular_mass 7774.992
_Mol_thiol_state 'all disulfide bound'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 68
_Mol_residue_sequence
;
SPYSSDTTPCCFAYIARPLP
RAHIKEYFYTSGKCSNPAVV
FVTRKNRQVCANPEKKWVRE
YINSLEMS
;
loop_
_Residue_seq_code
_Residue_label
1 SER 2 PRO 3 TYR 4 SER 5 SER
6 ASP 7 THR 8 THR 9 PRO 10 CYS
11 CYS 12 PHE 13 ALA 14 TYR 15 ILE
16 ALA 17 ARG 18 PRO 19 LEU 20 PRO
21 ARG 22 ALA 23 HIS 24 ILE 25 LYS
26 GLU 27 TYR 28 PHE 29 TYR 30 THR
31 SER 32 GLY 33 LYS 34 CYS 35 SER
36 ASN 37 PRO 38 ALA 39 VAL 40 VAL
41 PHE 42 VAL 43 THR 44 ARG 45 LYS
46 ASN 47 ARG 48 GLN 49 VAL 50 CYS
51 ALA 52 ASN 53 PRO 54 GLU 55 LYS
56 LYS 57 TRP 58 VAL 59 ARG 60 GLU
61 TYR 62 ILE 63 ASN 64 SER 65 LEU
66 GLU 67 MET 68 SER
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$ccl5 Human 9606 Eukaryota Metazoa Homo sapiens
stop_
save_
#########################
# Experimental source #
#########################
save_experimental_source
_Saveframe_category experimental_source
loop_
_Mol_label
_Production_method
_Host_organism_name_common
_Genus
_Species
_Strain
_Vector_name
$ccl5 'recombinant technology' . Escherichia coli BL21 pET-23
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Saveframe_category sample
_Sample_type solution
_Details 'isotropic sample'
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$ccl5 1 mM '[U-100% 15N]'
'sodium acetate' 50 mM 'natural abundance'
H2O 90 % 'natural abundance'
D2O 10 % 'natural abundance'
stop_
save_
save_sample_2
_Saveframe_category sample
_Sample_type 'gel solid'
_Details 'stretched neutral gel for alignment'
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$ccl5 1 mM '[U-100% 15N]'
'sodium acetate' 50 mM 'natural abundance'
polyacrylamide 5 % 'natural abundance'
H2O 90 % 'natural abundance'
D2O 10 % 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_NAMD
_Saveframe_category software
_Name NAMD
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Phillips, Braun, Wang, Gumbart, Tajkhorshid, Villa, Chipot, Skeel, Kale, and Schulte'
;
NAMD Team
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois
405 North Mathews MC-251
Urbana, Illinois 61801 USA
;
namd@ks.uiuc.edu
stop_
loop_
_Task
refinement
stop_
_Details 'molecular dynamics simulation'
save_
save_NMRView
_Saveframe_category software
_Name NMRView
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Johnson, One Moon Scientific' . .
stop_
loop_
_Task
'data analysis'
stop_
_Details .
save_
save_VNMRJ
_Saveframe_category software
_Name VNMRJ
_Version .
loop_
_Vendor
_Address
_Electronic_address
Varian . .
stop_
loop_
_Task
collection
stop_
_Details .
save_
save_VMD
_Saveframe_category software
_Name VMD
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Humphrey, Dalke & Schulten.'
;
VMD Team
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois
405 North Mathews MC-251
Urbana, Illinois 61801 USA
;
vmd@ks.uiuc.edu
stop_
loop_
_Task
refinement
stop_
_Details 'for constructing structures'
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Varian
_Model INOVA
_Field_strength 800
_Details .
save_
save_spectrometer_2
_Saveframe_category NMR_spectrometer
_Manufacturer Varian
_Model INOVA
_Field_strength 900
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_1H-15N_J-mod_TROSY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-15N J-mod TROSY'
_Sample_label $sample_1
save_
save_2D_1H-15N_TROSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-15N TROSY'
_Sample_label $sample_2
save_
save_2D_1H-15N_HSQC_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-15N HSQC'
_Sample_label $sample_2
save_
save_2D_1H-15N_J-mod_TROSY_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-15N J-mod TROSY'
_Sample_label $sample_2
save_
save_2D_1H-15N_HSQC_5
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-15N HSQC'
_Sample_label $sample_1
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
'ionic strength' 0.05 . M
pH 4.4 . pH
pressure 1 . atm
temperature 297 . K
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_reference_1
_Saveframe_category chemical_shift_reference
_Details .
loop_
_Mol_common_name
_Atom_type
_Atom_isotope_number
_Atom_group
_Chem_shift_units
_Chem_shift_value
_Reference_method
_Reference_type
_External_reference_sample_geometry
_External_reference_location
_External_reference_axis
_Indirect_shift_ratio
DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000
DSS N 15 'methyl protons' ppm 0.00 . indirect . . . 0.101329118
stop_
save_
###################################
# Assigned chemical shift lists #
###################################
###################################################################
# Chemical Shift Ambiguity Index Value Definitions #
# #
# The values other than 1 are used for those atoms with different #
# chemical shifts that cannot be assigned to stereospecific atoms #
# or to specific residues or chains. #
# #
# Index Value Definition #
# #
# 1 Unique (including isolated methyl protons, #
# geminal atoms, and geminal methyl #
# groups with identical chemical shifts) #
# (e.g. ILE HD11, HD12, HD13 protons) #
# 2 Ambiguity of geminal atoms or geminal methyl #
# proton groups (e.g. ASP HB2 and HB3 #
# protons, LEU CD1 and CD2 carbons, or #
# LEU HD11, HD12, HD13 and HD21, HD22, #
# HD23 methyl protons) #
# 3 Aromatic atoms on opposite sides of #
# symmetrical rings (e.g. TYR HE1 and HE2 #
# protons) #
# 4 Intraresidue ambiguities (e.g. LYS HG and #
# HD protons or TRP HZ2 and HZ3 protons) #
# 5 Interresidue ambiguities (LYS 12 vs. LYS 27) #
# 6 Intermolecular ambiguities (e.g. ASP 31 CA #
# in monomer 1 and ASP 31 CA in monomer 2 #
# of an asymmetrical homodimer, duplex #
# DNA assignments, or other assignments #
# that may apply to atoms in one or more #
# molecule in the molecular assembly) #
# 9 Ambiguous, specific ambiguity not defined #
# #
###################################################################
save_assigned_chem_shift_list_1
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D 1H-15N HSQC'
stop_
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_1
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name chain_1
_Text_data_format .
_Text_data .
loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 3 3 TYR H H 8.081 0.03 1
2 3 3 TYR N N 119.535 0.5 1
3 4 4 SER H H 8.299 0.03 1
4 4 4 SER N N 117.688 0.5 1
5 5 5 SER H H 8.123 0.03 1
6 5 5 SER N N 114.930 0.5 1
7 6 6 ASP H H 7.682 0.03 1
8 6 6 ASP N N 122.288 0.5 1
9 7 7 THR H H 7.975 0.03 1
10 7 7 THR N N 110.391 0.5 1
11 8 8 THR H H 9.270 0.03 1
12 8 8 THR N N 117.872 0.5 1
13 10 10 CYS H H 9.116 0.03 1
14 10 10 CYS N N 118.864 0.5 1
15 11 11 CYS H H 9.175 0.03 1
16 11 11 CYS N N 117.401 0.5 1
17 12 12 PHE H H 9.305 0.03 1
18 12 12 PHE N N 120.239 0.5 1
19 13 13 ALA H H 7.636 0.03 1
20 13 13 ALA N N 122.330 0.5 1
21 14 14 TYR H H 8.110 0.03 1
22 14 14 TYR N N 113.347 0.5 1
23 15 15 ILE H H 9.138 0.03 1
24 15 15 ILE N N 123.848 0.5 1
25 16 16 ALA H H 8.567 0.03 1
26 16 16 ALA N N 127.510 0.5 1
27 17 17 ARG H H 7.548 0.03 1
28 17 17 ARG N N 117.356 0.5 1
29 21 21 ARG H H 8.532 0.03 1
30 21 21 ARG N N 128.221 0.5 1
31 22 22 ALA H H 8.647 0.03 1
32 22 22 ALA N N 118.458 0.5 1
33 23 23 HIS H H 7.770 0.03 1
34 23 23 HIS N N 113.436 0.5 1
35 24 24 ILE H H 7.605 0.03 1
36 24 24 ILE N N 119.475 0.5 1
37 25 25 LYS H H 9.401 0.03 1
38 25 25 LYS N N 124.823 0.5 1
39 26 26 GLU H H 7.972 0.03 1
40 26 26 GLU N N 114.965 0.5 1
41 27 27 TYR H H 8.389 0.03 1
42 27 27 TYR N N 117.043 0.5 1
43 28 28 PHE H H 8.528 0.03 1
44 28 28 PHE N N 114.773 0.5 1
45 29 29 TYR H H 8.995 0.03 1
46 29 29 TYR N N 119.398 0.5 1
47 30 30 THR H H 8.083 0.03 1
48 30 30 THR N N 111.130 0.5 1
49 31 31 SER H H 9.753 0.03 1
50 31 31 SER N N 115.139 0.5 1
51 32 32 GLY H H 9.096 0.03 1
52 32 32 GLY N N 118.978 0.5 1
53 33 33 LYS H H 7.991 0.03 1
54 33 33 LYS N N 117.041 0.5 1
55 34 34 CYS H H 7.370 0.03 1
56 34 34 CYS N N 116.415 0.5 1
57 35 35 SER H H 8.771 0.03 1
58 35 35 SER N N 117.817 0.5 1
59 36 36 ASN H H 8.152 0.03 1
60 36 36 ASN N N 118.406 0.5 1
61 38 38 ALA H H 8.179 0.03 1
62 38 38 ALA N N 121.530 0.5 1
63 39 39 VAL H H 8.133 0.03 1
64 39 39 VAL N N 120.393 0.5 1
65 40 40 VAL H H 8.766 0.03 1
66 40 40 VAL N N 126.255 0.5 1
67 41 41 PHE H H 9.084 0.03 1
68 41 41 PHE N N 123.455 0.5 1
69 42 42 VAL H H 8.861 0.03 1
70 42 42 VAL N N 124.027 0.5 1
71 43 43 THR H H 9.364 0.03 1
72 43 43 THR N N 118.255 0.5 1
73 44 44 ARG H H 8.499 0.03 1
74 44 44 ARG N N 118.579 0.5 1
75 45 45 LYS H H 7.632 0.03 1
76 45 45 LYS N N 116.972 0.5 1
77 46 46 ASN H H 8.289 0.03 1
78 46 46 ASN N N 114.914 0.5 1
79 47 47 ARG H H 7.474 0.03 1
80 47 47 ARG N N 118.441 0.5 1
81 48 48 GLN H H 8.820 0.03 1
82 48 48 GLN N N 123.561 0.5 1
83 49 49 VAL H H 8.972 0.03 1
84 49 49 VAL N N 123.147 0.5 1
85 50 50 CYS H H 9.030 0.03 1
86 50 50 CYS N N 125.424 0.5 1
87 51 51 ALA H H 9.806 0.03 1
88 51 51 ALA N N 124.859 0.5 1
89 52 52 ASN H H 8.202 0.03 1
90 52 52 ASN N N 120.149 0.5 1
91 54 54 GLU H H 7.567 0.03 1
92 54 54 GLU N N 113.847 0.5 1
93 55 55 LYS H H 7.237 0.03 1
94 55 55 LYS N N 117.814 0.5 1
95 56 56 LYS H H 8.781 0.03 1
96 56 56 LYS N N 125.069 0.5 1
97 57 57 TRP H H 8.123 0.03 1
98 57 57 TRP N N 115.108 0.5 1
99 59 59 ARG H H 7.213 0.03 1
100 59 59 ARG N N 118.397 0.5 1
101 60 60 GLU H H 8.339 0.03 1
102 60 60 GLU N N 118.527 0.5 1
103 61 61 TYR H H 8.571 0.03 1
104 61 61 TYR N N 122.302 0.5 1
105 62 62 ILE H H 8.384 0.03 1
106 62 62 ILE N N 119.491 0.5 1
107 63 63 ASN H H 7.893 0.03 1
108 63 63 ASN N N 118.212 0.5 1
109 64 64 SER H H 7.909 0.03 1
110 64 64 SER N N 113.936 0.5 1
111 65 65 LEU H H 7.948 0.03 1
112 65 65 LEU N N 122.865 0.5 1
113 66 66 GLU H H 8.076 0.03 1
114 66 66 GLU N N 114.599 0.5 1
115 67 67 MET H H 8.044 0.03 1
116 67 67 MET N N 121.849 0.5 1
117 68 68 SER N N 122.500 0.5 1
stop_
save_