BMRB Entry 16961

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16961
MolProbity Validation Chart

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Title:
Solution NMR structure of Dsy0195(21-82) protein from Desulfitobacterium Hafniense. Northeast Structural Genomics Consortium Target DhR8C.
Deposition date:
2010-05-27
Original release date:
2012-08-02
Authors:
Yang, Yunhuang; Ramelot, Theresa; Cort, John; Wang, Huang; Ciccosanti, Colleen; Foote, Erica; Jiang, Mei; Janjua, Haleema; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael
Citation:

Citation: Yang, Yunhuang; Ramelot, Theresa; Cort, John; Wang, Huang; Ciccosanti, Colleen; Foote, Erica; Jiang, Mei; Janjua, Haleema; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly"  J. Struct. Funct. Genomics 12, 175-179 (2011).
PubMed: 21904870

Assembly members:

Assembly members:
Dsy0195(21-82)_protein, polymer, 71 residues, 13583.6 Da.

Natural source:

Natural source:   Common Name: Desulfitobacterium Hafniense   Taxonomy ID: 49338   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Desulfitobacterium Hafniense

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET 21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dsy0195(21-82)_protein: MDNRQFLSLTGVSKVQSFDP KEILLETIQGVLSIKGEKLG IKHLDLKAGQVEVEGLIDAL VYPLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts289
15N chemical shifts69
1H chemical shifts482

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Dsy0195(21-82) protein1

Entities:

Entity 1, Dsy0195(21-82) protein 71 residues - 13583.6 Da.

residues 21-82 of Dsy0195(21-82) protein from Desulfitobacterium Hafniense, preceded by non-native N-terminal Met and followed by 8 non-native C-terminal residues (LEHHHHHH)

1   METASPASNARGGLNPHELEUSERLEUTHR
2   GLYVALSERLYSVALGLNSERPHEASPPRO
3   LYSGLUILELEULEUGLUTHRILEGLNGLY
4   VALLEUSERILELYSGLYGLULYSLEUGLY
5   ILELYSHISLEUASPLEULYSALAGLYGLN
6   VALGLUVALGLUGLYLEUILEASPALALEU
7   VALTYRPROLEUGLUHISHISHISHISHIS
8   HIS

Samples:

NC_sample: Dsy0195(21-82) protein, [U-100% 13C; U-100% 15N], 1.0 ± 0.1 mM; ammonium acetate 20 ± 1 mM; sodium chloride 200 ± 10 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %

NC5_sample: Dsy0195(21-82) protein, [U-5% 13C; U-100% 15N], 1 ± 0.09 mM; ammonium acetate 20 ± 1 mM; sodium chloride 200 ± 10 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %

NC_sample_in_D2O: Dsy0195(21-82) protein, [U-100% 13C; U-100% 15N], 1.0 ± 0.1 mM; ammonium acetate 20 ± 1 mM; sodium chloride 200 ± 10 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %

NC50_sample: Dsy0195(21-82) protein, [U-100% 13C; U-100% 15N], 1.0 ± 0.1 mM; Dsy0195(21-82) protein 1.0 ± 0.1 mM; ammonium acetate 20 ± 1 mM; sodium chloride 200 ± 10 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %

sample_conditions_1: ionic strength: 0.2 M; pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQCNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC_CTNC5_sampleisotropicsample_conditions_1
3D 1H-15N NOESYNC_sampleisotropicsample_conditions_1
3D 1H-13C NOESYNC_sampleisotropicsample_conditions_1
3D HNCONC_sampleisotropicsample_conditions_1
3D HNCANC_sampleisotropicsample_conditions_1
3D HNCACBNC_sampleisotropicsample_conditions_1
3D CBCA(CO)NHNC_sampleisotropicsample_conditions_1
3D HN(CO)CANC_sampleisotropicsample_conditions_1
3D HBHA(CO)NHNC_sampleisotropicsample_conditions_1
3D H(CCO)NHNC_sampleisotropicsample_conditions_1
3D C(CO)NHNC_sampleisotropicsample_conditions_1
3D HCCH-TOCSYNC_sampleisotropicsample_conditions_1
3D HCCH-COSYNC_sampleisotropicsample_conditions_1
3D (H)CCH-TOCSYNC_sample_in_D2Oisotropicsample_conditions_1
4D CC NOESYNC_sample_in_D2Oisotropicsample_conditions_1
3D edited/filtered CnoesyNC50_sampleisotropicsample_conditions_1
2D 1H-15N HSQC_HistidineNC_sampleisotropicsample_conditions_1
2D 1H-15N HSQC_swN150ppmNC_sampleisotropicsample_conditions_1

Software:

NMRPipe v2008, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMR v6.1C, Varian - collection

TOPSPIN v2.1.3, Bruker Biospin - collection

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - data analysis

X-PLOR NIH v2.20, Schwieters, Kuszewski, Tjandra and Clore - structure solution

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

SPARKY v3.113, Goddard - data analysis

PSVS v1.4, Bhattacharya and Montelione - refinement

AutoAssign v2.30, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

PDBStat v5.1, (PdbStat)-Roberto Tejero and Gaetano T. Montelione - structure solution

CYANA v2.1.3, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure solution

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker AvanceIII 850 MHz

Related Database Links:

BMRB 16656
PDB
DBJ BAE81984
EMBL CDX00176
GB ACL18206 EHL08222
REF WP_015942592

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks