BMRB Entry 16237

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16237
MolProbity Validation Chart

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Title:
Solution structure of the amino-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis.
Deposition date:
2009-04-02
Original release date:
2011-06-01
Authors:
Yang, Yinshan; Auguin, Daniel; Delbecq, Stephane; Dumas, Emilie; Molle, Virginie; Saint, Nathalie
Citation:

Citation: Yang, Yinshan; Auguin, Daniel; Delbecq, Stephane; Dumas, Emilie; Molle, Gerard; Molle, Virginie; Roumestand, Christian; Saint, Nathalie. "Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an oligomeric channel in the mycobacterial cell wall."  Proteins 79, 645-661 (2011).
PubMed: 21117233

Assembly members:

Assembly members:
amino-terminal domain, polymer, 254 residues, 13602.4 Da.

Natural source:

Natural source:   Common Name: Mycobacterium tuberculosis   Taxonomy ID: 1773   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Mycobacterium tuberculosis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pETSIG-ompATb73-326

Entity Sequences (FASTA):

Entity Sequences (FASTA):
amino-terminal domain: GASALSLSLLSISRSGNTVT LIGDFPDEAAKAALMTALNG LLAPGVNVIDQIHVDPVVRS LDFSSAEPVFTASVPIPDFG LKVERDTVTLTGTAPSSEHK DAVKRAATSTWPDMKIVNNI EVTGQAPPGPPASGPCADLQ SAINAVTGGPIAFGNDGASL IPADYEILNRVADKLKACPD ARVTINGYTDNTGSEGINIP LSAQRAKIVADYLVARGVAG DHIATVGLGSVNPIASNATP EGRAKNRRVEIVVN

Data sets:
Data typeCount
13C chemical shifts579
15N chemical shifts235
1H chemical shifts1482

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1amino-terminal domain1

Entities:

Entity 1, amino-terminal domain 254 residues - 13602.4 Da.

1   GLYALASERALALEUSERLEUSERLEULEU
2   SERILESERARGSERGLYASNTHRVALTHR
3   LEUILEGLYASPPHEPROASPGLUALAALA
4   LYSALAALALEUMETTHRALALEUASNGLY
5   LEULEUALAPROGLYVALASNVALILEASP
6   GLNILEHISVALASPPROVALVALARGSER
7   LEUASPPHESERSERALAGLUPROVALPHE
8   THRALASERVALPROILEPROASPPHEGLY
9   LEULYSVALGLUARGASPTHRVALTHRLEU
10   THRGLYTHRALAPROSERSERGLUHISLYS
11   ASPALAVALLYSARGALAALATHRSERTHR
12   TRPPROASPMETLYSILEVALASNASNILE
13   GLUVALTHRGLYGLNALAPROPROGLYPRO
14   PROALASERGLYPROCYSALAASPLEUGLN
15   SERALAILEASNALAVALTHRGLYGLYPRO
16   ILEALAPHEGLYASNASPGLYALASERLEU
17   ILEPROALAASPTYRGLUILELEUASNARG
18   VALALAASPLYSLEULYSALACYSPROASP
19   ALAARGVALTHRILEASNGLYTYRTHRASP
20   ASNTHRGLYSERGLUGLYILEASNILEPRO
21   LEUSERALAGLNARGALALYSILEVALALA
22   ASPTYRLEUVALALAARGGLYVALALAGLY
23   ASPHISILEALATHRVALGLYLEUGLYSER
24   VALASNPROILEALASERASNALATHRPRO
25   GLUGLYARGALALYSASNARGARGVALGLU
26   ILEVALVALASN

Samples:

sample_0: entity mM; sodium phosphate 50 mM

sample_1: entity, [U-99% 15N], mM; sodium phosphate 50 mM

sample_2: entity, [U-99% 15N, U-99% 13C], mM; sodium phosphate 50 mM

sample_4: entity, [U-99% 15N], mM; sodium phosphate 50 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6; pressure: 1.0 atm; temperature: 300 K

sample_conditions_2: ionic strength: 100 mM; pH: 6; pressure: 1.0 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_0isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_0isotropicsample_conditions_2

Software:

AMBER v8, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

GIFA, Delsuc - processing

xwinnmr, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

BMRB 16846 17575 17863
PDB
DBJ BAH25212 BAL64801 BAQ04819 GAA44658
EMBL CAL70937 CCC25980 CCC43237 CCC63509 CCE36433
GB AAK45169 ABI54278 ABQ72638 ABR05261 ACT26182
REF NP_215414 NP_854580 WP_003404684 WP_003915129 WP_014000491
SP A1KH31 P65594 P9WIU4 P9WIU5
AlphaFold A1KH31 P65594 P9WIU4 P9WIU5

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