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- PDB-2lrg: NMR structure of the protein YP_001300941.1 from Bacteroides vulgatus -

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Basic information

Entry
Database: PDB / ID: 2lrg
TitleNMR structure of the protein YP_001300941.1 from Bacteroides vulgatus
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homologyLipoxygenase-1 - #60 / PLAT/LH2 and C2-like Ca2+-binding lipoprotein / PLAT/LH2 and C2-like Ca2+-binding lipoprotein / Lipoxygenase-1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Sandwich / Mainly Beta / Lipoprotein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 2
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein YP_001300941.1 from Bacteroides vulgatus
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionMar 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,4881
Polymers13,4881
Non-polymers00
Water0
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 Uncharacterized protein


Mass: 13487.908 Da / Num. of mol.: 1 / Fragment: UNP residues 30-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_3708 / Production host: Escherichia coli (E. coli) / References: UniProt: A6L6K5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1214D APSY-HACANH
1315D APSY-(HA)CA(CO)NH
1415D APSY-CBCA(CO)NH
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 95 mM H2O, 5 mM [U-99% 2H] D2O, 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
20 mMsodium phosphate-21
50 mMsodium chloride-31
95 mMH2O-41
5 mMD2O-5[U-99% 2H]1
Sample conditionsIonic strength: 0.08 / pH: 6.0 / 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
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
UNIO(Unio)-Herrmann and Wuthrichstructure solution
UNIO(Unio)-Herrmann and Wuthrichchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2147 / NOE intraresidue total count: 488 / NOE long range total count: 860 / NOE medium range total count: 186 / NOE sequential total count: 613
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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