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- PDB-2mca: NMR structure of the protein YP_002937094.1 from Eubacterium rectale -

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Basic information

Entry
Database: PDB / ID: 2mca
TitleNMR structure of the protein YP_002937094.1 from Eubacterium rectale
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homologyDomain of unknown function DUF5300 / Domain of unknown function (DUF5300) / Domain of unknown function (DUF5300) / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesEubacterium rectale (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model18
AuthorsProudfoot, A. / Serrano, P. / Geralt, M. / Dutta, S. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein YP_002937094.1 from Eubacterium rectale
Authors: Proudfoot, A. / Wuthrich, K. / Serrano, P. / Geralt, M. / Dutta, S.K.
History
DepositionAug 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Other
Revision 1.2Jun 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

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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)11,3581
Polymers11,3581
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: 11358.426 Da / Num. of mol.: 1 / Fragment: UNP residues 32-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_1200 / Production host: Escherichia coli (E. coli) / References: UniProt: C4ZHE8

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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, 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
Sample conditionsIonic strength: 0.220 / 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
UNIOHerrmann and Wuthrichstructure solution
UNIOHerrmann and Wuthrichchemical shift assignment
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
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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