BMRB Entry 15651

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15651
MolProbity Validation Chart

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Title:
NMR structure of the transmembrane domain of the Outer Membrane Protein A from Klebsiella pneumoniae in DHPC micelles.
Deposition date:
2008-02-04
Original release date:
2008-11-04
Authors:
Renault, Marie; Saurel, Olivier; Gervais, Virginie; Lohr, Franck; Reat, Valerie; Piotto, Martial; Milon, Alain
Citation:

Citation: Renault, Marie; Saurel, Olivier; Czaplicki, Jerzy; Demange, Pascal; Gervais, Virginie; Lohr, Frank; Reat, Valerie; Piotto, Martial; Milon, Alain. "Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications"  J. Mol. Biol. 385, 117-130 (2009).
PubMed: 18952100

Assembly members:

Assembly members:
KpOmpA_transmembrane_domain, polymer, 216 residues, 23367.7 Da.

Natural source:

Natural source:   Common Name: Klebsiella pneumoniae   Taxonomy ID: 573   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Klebsiella pneumoniae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET21c-KpOmpA

Entity Sequences (FASTA):

Entity Sequences (FASTA):
KpOmpA_transmembrane_domain: ARIMKAIFVLNAAPKDNTWY AGGKLGWSQYHDTGFYGNGF QNNNGPTRNDQLGAGAFGGY QVNPYLGFEMGYDWLGRMAY KGSVDNGAFKAQGVQLTAKL GYPITDDLDIYTRLGGMVWR ADSKGNYASTGVSRSEHDTG VSPVFAGGVEWAVTRDIATR LEYQWVNNIGDAGTVGTRPD NGMLSLGVSYRFGQEDAAPV VAPAPAPAPEHHHHHH

Data sets:
Data typeCount
13C chemical shifts673
15N chemical shifts170
1H chemical shifts359

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1KpOmpA transmembrane domain1

Entities:

Entity 1, KpOmpA transmembrane domain 216 residues - 23367.7 Da.

Residues 1-3 represent a non-native cloning tag and residues 211-216 represent a non-native affinity tag.

1   ALAARGILEMETLYSALAILEPHEVALLEU
2   ASNALAALAPROLYSASPASNTHRTRPTYR
3   ALAGLYGLYLYSLEUGLYTRPSERGLNTYR
4   HISASPTHRGLYPHETYRGLYASNGLYPHE
5   GLNASNASNASNGLYPROTHRARGASNASP
6   GLNLEUGLYALAGLYALAPHEGLYGLYTYR
7   GLNVALASNPROTYRLEUGLYPHEGLUMET
8   GLYTYRASPTRPLEUGLYARGMETALATYR
9   LYSGLYSERVALASPASNGLYALAPHELYS
10   ALAGLNGLYVALGLNLEUTHRALALYSLEU
11   GLYTYRPROILETHRASPASPLEUASPILE
12   TYRTHRARGLEUGLYGLYMETVALTRPARG
13   ALAASPSERLYSGLYASNTYRALASERTHR
14   GLYVALSERARGSERGLUHISASPTHRGLY
15   VALSERPROVALPHEALAGLYGLYVALGLU
16   TRPALAVALTHRARGASPILEALATHRARG
17   LEUGLUTYRGLNTRPVALASNASNILEGLY
18   ASPALAGLYTHRVALGLYTHRARGPROASP
19   ASNGLYMETLEUSERLEUGLYVALSERTYR
20   ARGPHEGLYGLNGLUASPALAALAPROVAL
21   VALALAPROALAPROALAPROALAPROGLU
22   HISHISHISHISHISHIS

Samples:

sample_1: KpOmpA transmembrane domain, [U-13C; U-15N; U-2H], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%

sample_2: KpOmpA transmembrane domain, [U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%

sample_3: KpOmpA transmembrane domain, [U-15N; 10% 13C], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%

sample_4: KpOmpA transmembrane domain, [U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3], 1 mM; DHPC 300 mM; NaH2PO4 20 mM; NaCl 100 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 313 K

Experiments:

NameSampleSample stateSample conditions
2D [15N,1H]-TROSYsample_1isotropicsample_conditions_1
3D [15N,1H]-TROSY-HNCACBsample_1isotropicsample_conditions_1
3D [15N,1H]-TROSY-HN(CO)CACBsample_1isotropicsample_conditions_1
3D [15N,1H]-TROSY-HNCOsample_1isotropicsample_conditions_1
3D [15N,1H]-TROSY-HN(CA)COsample_1isotropicsample_conditions_1
3D (HNCA)CC-TOCSY-(CA)-[15N,1H]-TROSYsample_1isotropicsample_conditions_1
3D (H)C(CC)-TOCSY-(CA)-[15N,1H]-TROSYsample_2isotropicsample_conditions_1
3D H(CCCO)-TOCSYsample_2isotropicsample_conditions_1
2D [1H,13C]-CT-HSQCsample_3isotropicsample_conditions_1
4D 15N,15N-separated HMQC-NOESY-TROSYsample_1isotropicsample_conditions_1
3D 15N,13C-separated HMQC-NOESY-TROSYsample_4isotropicsample_conditions_1
3D 13C,13C-separated HMQC-NOESYsample_4isotropicsample_conditions_1

Software:

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

NMRView vv5.2.2, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

PDB
DBJ BAH62679
EMBL CAA04450 CCI75899 CCM81556 CCM88663 CCM94835
GB ABR76422 AEJ97514 AEW60563 AFQ66532 AGT24954
PIR JC6558
REF WP_002898408 WP_004201430 WP_004219211 WP_016529119 WP_032432880
SP P24017
AlphaFold P24017

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