BMRB Entry 16629

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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/BMR16629
MolProbity Validation Chart

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Title:
solution structure of Helicobacter pylori SlyD
Deposition date:
2009-12-07
Original release date:
2012-08-03
Authors:
Cheng, Tianfan; Li, Hongyan; Xia, Wei; Sze, Kong Hung; Sun, Hongzhe
Citation:

Citation: Cheng, Tianfan; Li, Hongyan; Xia, Wei; Sze, Kong Hung; Sun, Hongzhe. "Structural and functional study of SlyD from helicobacter pylori"  J. Am. Chem. Soc. ., .-..

Assembly members:

Assembly members:
SlyD, polymer, 151 residues, 17039.195 Da.

Natural source:

Natural source:   Common Name: Helicobacter pylori   Taxonomy ID: 210   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Helicobacter pylori

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-32a(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SlyD: MQNHDLESIKQAALIEYEVR EQGSSIVLDSNISKEPLEFI IGTNQIIAGLEKAVLKAQIG EWEEVVIAPEEAYGVYESSY LQEVPRDQFEGIELEKGMSV FGQTEDNQTIQAIIKDFSAT HVMVDYNHPLAGKTLAFRFK VLGFREVSEEE

Data sets:
Data typeCount
13C chemical shifts655
15N chemical shifts161
1H chemical shifts1083

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1SlyD1

Entities:

Entity 1, SlyD 151 residues - 17039.195 Da.

1   METGLNASNHISASPLEUGLUSERILELYS
2   GLNALAALALEUILEGLUTYRGLUVALARG
3   GLUGLNGLYSERSERILEVALLEUASPSER
4   ASNILESERLYSGLUPROLEUGLUPHEILE
5   ILEGLYTHRASNGLNILEILEALAGLYLEU
6   GLULYSALAVALLEULYSALAGLNILEGLY
7   GLUTRPGLUGLUVALVALILEALAPROGLU
8   GLUALATYRGLYVALTYRGLUSERSERTYR
9   LEUGLNGLUVALPROARGASPGLNPHEGLU
10   GLYILEGLULEUGLULYSGLYMETSERVAL
11   PHEGLYGLNTHRGLUASPASNGLNTHRILE
12   GLNALAILEILELYSASPPHESERALATHR
13   HISVALMETVALASPTYRASNHISPROLEU
14   ALAGLYLYSTHRLEUALAPHEARGPHELYS
15   VALLEUGLYPHEARGGLUVALSERGLUGLU
16   GLU

Samples:

sample_1: SlyD, [U-100% 13C; U-100% 15N], 1 – 1.5 mM; Tris buffer 20 mM; NaCl 100 mM; NaN3 0.02%; H2O 90%; D2O 10%

sample_2: SlyD, [U-100% 13C; U-100% 15N], 1 – 1.5 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_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 C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

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

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAJ58642 BAM96994 BAO97129
EMBL CBI65934
GB AAD08168 ABF85129 ACX99620 ADO07305 ADU80316
REF NP_207914 WP_001179275 WP_001179276 WP_001179277 WP_001179282
SP O25748
AlphaFold O25748

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