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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 19752

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19752
MolProbity Validation Chart

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Title: Solution structure of a protein domain   PubMed: 24831957

Deposition date: 2014-01-24 Original release date: 2014-05-27

Authors: Feng, Yingang; Gu, Jingmin

Citation: Gu, Jingmin; Feng, Yingang; Feng, Xin; Sun, Changjiang; Lei, Liancheng; Ding, Wei; Niu, Fengfeng; Jiao, Lianying; Yang, Mei; Li, Yue; Liu, Xiaohe; Song, Jun; Cui, Ziyin; Han, Dong; Du, Chongtao; Yang, Yongjun; Ouyang, Songying; Liu, Zhi-Jie; Han, Wenyu. "Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented "EF-Hand-Like" Calcium-Binding Phage Lysin"  Plos Pathog. 10, e1004109-e1004109 (2014).

Assembly members:
entity, polymer, 131 residues, 14048.874 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: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity: SNAKNYMDKGTSSSTVVKDG KTSSASTPATRPVTGSWKKN QYGTWYKPENATFVNGNQPI VTRIGSPFLNAPVGGNLPAG ATIVYDEVCIQAGHIWIGYN AYNGNRVYCPVRTCQGVPPN HIPGVAWGVFK

Data sets:
Data typeCount
13C chemical shifts560
15N chemical shifts136
1H chemical shifts869

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 131 residues - 14048.874 Da.

1   SERASNALALYSASNTYRMETASPLYSGLY
2   THRSERSERSERTHRVALVALLYSASPGLY
3   LYSTHRSERSERALASERTHRPROALATHR
4   ARGPROVALTHRGLYSERTRPLYSLYSASN
5   GLNTYRGLYTHRTRPTYRLYSPROGLUASN
6   ALATHRPHEVALASNGLYASNGLNPROILE
7   VALTHRARGILEGLYSERPROPHELEUASN
8   ALAPROVALGLYGLYASNLEUPROALAGLY
9   ALATHRILEVALTYRASPGLUVALCYSILE
10   GLNALAGLYHISILETRPILEGLYTYRASN
11   ALATYRASNGLYASNARGVALTYRCYSPRO
12   VALARGTHRCYSGLNGLYVALPROPROASN
13   HISILEPROGLYVALALATRPGLYVALPHE
14   LYS

Samples:

sample_1: entity, [U-13C; U-15N], 1.1 mM; sodium phosphate 40 mM; sodium chloride 50 mM; DSS 0.02%; D2O 10%; H2O 90%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

NMR spectrometers:

  • Agilent DD2 600 MHz

Related Database Links:

PDB
DBJ BAO09229 BAO09443 BAO47098
EMBL CCA65933
GB AAO47477 AAX92142 ABL87139 ACB89049 ADG26756
REF YP_007002194 YP_007112796 YP_008854024 YP_008854201 YP_008873573

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