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- PDB-2mhd: NMR structure of the protein BACUNI_03114 from Bacteroides unifor... -

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Basic information

Entry
Database: PDB / ID: 2mhd
TitleNMR structure of the protein BACUNI_03114 from Bacteroides uniformis ATCC 8492
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / Lipocalin 4 / Beta barrel / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homologyLipocalin - #370 / Lipocalin-like domain / Lipocalin-like domain / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / Lipocalin-like domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model8
AuthorsShnitkind, S. / Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein BACUNI_03114 from Bacteroides uniformis ATCC 8492
Authors: Shnitkind, S. / Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionNov 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references / Structure summary
Revision 1.2Sep 9, 2020Group: Data collection / Database references
Category: citation / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.title / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,8141
Polymers12,8141
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)19 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein


Mass: 12814.306 Da / Num. of mol.: 1 / Fragment: UNP residues 24-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_03114 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: A7V6A1

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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 HACANH APSY
1315D (HA)CA(CO)NH APSY
1415D CBCA(CO)NH APSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM sodium azide, 1.2 mM [U-99% 13C; U-99% 15N] protein, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
50 mMsodium chloride-21
5 mMsodium azide-31
1.2 mMentity-4[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0.0798 / 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
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospindata analysis
TopSpin2.1Bartels et al.collection
TopSpin2.1Bartels et al.processing
TopSpin2.1Bartels et al.data analysis
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospindata analysis
TopSpin2.1Bartels et al.collection
TopSpin2.1Bartels et al.processing
TopSpin2.1Bartels et al.data analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
j-UNIOHerrmann, Guntert and Wuthrichchemical shift assignment
j-UNIOHerrmann, Guntert and Wuthrichpeak picking
j-UNIOHerrmann, Guntert and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1733 / NOE intraresidue total count: 469 / NOE long range total count: 603 / NOE medium range total count: 168 / NOE sequential total count: 493
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 19

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