BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 16400

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16400
MolProbity Validation Chart

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Title: SOLUTION STRUCTURE OF AN ABC COLLAGEN HETEROTRIMER REVEALS A SINGLE-REGISTER HELIX STABILIZED BY ELECTROSTATIC INTERACTIONS   PubMed: 19625247

Deposition date: 2009-07-09 Original release date: 2009-09-04

Authors: Fallas, Jorge; Gauba, Varun; Hartgerink, Jeffrey

Citation: Fallas, Jorge; Gauba, Varun; Hartgerink, Jeffrey. "Solution structure of an ABC collagen heterotrimer reveals a single-register helix stabilized by electrostatic interactions."  J. Biol. Chem. 284, 26851-26859 (2009).

Assembly members:
collagen A, polymer, 30 residues, 2849.519 Da.
collagen B, polymer, 30 residues, 2868.582 Da.
collagen C, polymer, 30 residues, 2688.862 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
collagen A: PKGPKGPKGPKGPKGPKGPK GPKGPKGPKG
collagen B: DXGDXGDXGDXGDXGDXGDX GDXGDXGDXG
collagen C: PXGPXGPXGPXGPXGPXGPX GPXGPXGPXG

Data sets:
Data typeCount
13C chemical shifts18
15N chemical shifts5
1H chemical shifts46

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1collagen A1
2collagen B2
3collagen C3

Entities:

Entity 1, collagen A 30 residues - 2849.519 Da.

1   PROLYSGLYPROLYSGLYPROLYSGLYPRO
2   LYSGLYPROLYSGLYPROLYSGLYPROLYS
3   GLYPROLYSGLYPROLYSGLYPROLYSGLY

Entity 2, collagen B 30 residues - 2868.582 Da.

1   ASPHYPGLYASPHYPGLYASPHYPGLYASP
2   HYPGLYASPHYPGLYASPHYPGLYASPHYP
3   GLYASPHYPGLYASPHYPGLYASPHYPGLY

Entity 3, collagen C 30 residues - 2688.862 Da.

1   PROHYPGLYPROHYPGLYPROHYPGLYPRO
2   HYPGLYPROHYPGLYPROHYPGLYPROHYP
3   GLYPROHYPGLYPROHYPGLYPROHYPGLY

Samples:

sample_1: entity_1 1.2 mM; H2O 90%; D2O 10%

sample_2: entity_2 1.2 mM; H2O 90%; D2O 10%

sample_3: entity_3 1.2 mM; H2O 90%; D2O 10%

sample_4: entity_1 1.2 mM; entity_2 1.2 mM; entity_3 1.2 mM; H2O 90%; D2O 10%

sample_5: entity_1, [U-99% 13C; U-99% 15N], 1.2 mM; entity_2, [U-99% 13C; U-99% 15N], 1.2 mM; entity_3, [U-99% 13C; U-99% 15N], 1.2 mM; H2O 90%; D2O 10%; phosphate buffer 10 mM

sample_6: entity_1 1.8 mM; entity_2 1.2 mM; entity_3 1.2 mM; H2O 90%; D2O 10%; phosphate buffer 10 mM

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: pH: 7; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
3D HNHAsample_5isotropicsample_conditions_1
2D 1H-1H 13C-HMQC NOESY 15N-HSQCsample_5isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_2
2D 1H-1H TOCSYsample_4isotropicsample_conditions_2
2D 1H-15N HSQCsample_6isotropicsample_conditions_1

Software:

CNS vv 1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

SPARKY, Goddard - chemical shift assignment

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

CcpNMR, CCPN - data analysis

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

NMR spectrometers:

  • Varian INOVA 800 MHz

Related Database Links:

PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts