BMRB Entry 30515

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30515
MolProbity Validation Chart

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Title:
NMR solution structure of lanmodulin (LanM) complexed with yttrium(III) ions
Deposition date:
2018-09-19
Original release date:
2018-10-31
Authors:
Cook, E.; Featherson, E.; Showalter, S.; Cotruvo Jr., J.
Citation:

Citation: Cook, E.; Featherston, E.; Showalter, S.; Cotruvo Jr., J.. "Structural basis for rare earth element recognition by Methylobacterium extorquens lanmodulin."  Biochemistry 58, 120-125 (2018).
PubMed: 30352145

Assembly members:

Assembly members:
entity_1, polymer, 117 residues, 12529.771 Da.
entity_YT3, non-polymer, 88.906 Da.

Natural source:

Natural source:   Common Name: Methylobacterium extorquens   Taxonomy ID: 272630   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Methylobacterium extorquens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: PTTTTKVDIAAFDPDKDGTI DLKEALAAGSAAFDKLDPDK DGTLDAKELKGRVSEADLKK LDPDNDGTLDKKEYLAAVEA QFKAANPDNDGTIDARELAS PAGSALVNLIRHHHHHH

Data sets:
Data typeCount
13C chemical shifts300
15N chemical shifts100
1H chemical shifts598

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_2, 12
3entity_2, 22
4entity_2, 32
5entity_2, 42

Entities:

Entity 1, entity_1 117 residues - 12529.771 Da.

1   PROTHRTHRTHRTHRLYSVALASPILEALA
2   ALAPHEASPPROASPLYSASPGLYTHRILE
3   ASPLEULYSGLUALALEUALAALAGLYSER
4   ALAALAPHEASPLYSLEUASPPROASPLYS
5   ASPGLYTHRLEUASPALALYSGLULEULYS
6   GLYARGVALSERGLUALAASPLEULYSLYS
7   LEUASPPROASPASNASPGLYTHRLEUASP
8   LYSLYSGLUTYRLEUALAALAVALGLUALA
9   GLNPHELYSALAALAASNPROASPASNASP
10   GLYTHRILEASPALAARGGLULEUALASER
11   PROALAGLYSERALALEUVALASNLEUILE
12   ARGHISHISHISHISHISHIS

Entity 2, entity_2, 1 - Y - 88.906 Da.

1   YT3

Samples:

sample_1: Lanmodulin, [U-99% 13C; U-99% 15N], 1.14 mM; MOPS 20 mM; KCl 20 mM; acetate 5 mM; EGTA 1 mM; YCl3 5 mM

sample_2: Lanmodulin, [U-99% 13C; U-99% 15N], 1.26 mM; MOPS 20 mM; KCl 20 mM; acetate 5 mM; EGTA 1 mM; YCl3 5 mM

sample_conditions_1: ionic strength: 46 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

ARIA, Linge, O'Donoghue and Nilges - chemical shift assignment

SPARKY, Goddard - peak picking

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

NMR spectrometers:

  • Bruker AvanceIII 850 MHz

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