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- PDB-2mw1: NMR structure of the protein NP_809137.1 from Bacteroides thetaio... -

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Basic information

Entry
Database: PDB / ID: 2mw1
TitleNMR structure of the protein NP_809137.1 from Bacteroides thetaiotaomicron
ComponentsLipocalin-like protein
KeywordsStructural genomics / Unknown Function / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipocalin-like protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model6
AuthorsProudfoot, A. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein NP_809137.1 from Bacteroides thetaiotaomicron
Authors: Proudfoot, A. / Wuthrich, K. / Serrano, P. / Geralt, M. / Dutta, S.K.
History
DepositionOct 27, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin-like protein


Theoretical massNumber of molelcules
Total (without water)13,1901
Polymers13,1901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Lipocalin-like protein


Mass: 13189.693 Da / Num. of mol.: 1 / Fragment: Residues 18-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0224 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AB86

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D 1H-15N NOESY
151APSY 4D-HACANH
161APSY 5D-CBCA(CO)NH
171APSY 5D-(HA)CA(CO)NH

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 50 mM sodium chloride, 20 mM sodium phosphate, 5 mM sodium azide, 5 mM [U-99% 2H] DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-98% 13C; U-98% 15N]1
50 mMsodium chloride-21
20 mMsodium phosphate-31
5 mMsodium azide-41
5 mMDTT-5[U-99% 2H]1
Sample conditionsIonic strength: 0.22 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAHerrmann, Guntert and Wuthrichrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
UNIOHerrmann and Wuthrichchemical shift assignment
UNIOHerrmann and Wuthrichstructure solution
MddNMRMaxim Mayzel, Vladislav Orekhovprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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