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- PDB-2l6o: NMR structure of the protein YP_926445.1 from Shewanella Amazonensis -

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Basic information

Entry
Database: PDB / ID: 2l6o
TitleNMR structure of the protein YP_926445.1 from Shewanella Amazonensis
Componentsuncharacterized protein YP_926445.1
KeywordsStructure Genomics / unknown function / Structural Genomics / PSI-Biology / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


Uncharacterised protein PF13642 yp_926445, C-terminal domain / Uncharacterised protein PF13642 yp_926445, N-terminal domain / Protein of unknown function DUF4144 / protein structure with unknown function / Helicase, Ruva Protein; domain 3 / Thrombin, subunit H / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesShewanella amazonensis (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 4
AuthorsSerrano, P. / Geralt, M. / Mohanty, B. / Horst, R. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein YP_926445.1 from Shewanella Amazonensis
Authors: Serrano, P. / Geralt, M. / Mohanty, B. / Horst, R. / Wuthrich, K.
History
DepositionNov 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: uncharacterized protein YP_926445.1


Theoretical massNumber of molelcules
Total (without water)12,7941
Polymers12,7941
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 uncharacterized protein YP_926445.1


Mass: 12793.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: Sama_0567 / Plasmid: pSpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A1S319

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of the protein YP_926445.1 from Shewanella Amazonensis
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY (ali)
1513D 1H-15N NOESY (Aro)
1615D APSY-(HA)CA(CO)NH
1714D APSY-HACANH
1815D APSY-CBCA(CO)NH

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Sample preparation

DetailsContents: 20 mM sodium phosphate, 50 mM sodium chloride, 8 mM DTT, 4.5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
50 mMsodium chloride-21
8 mMDTT-31
4.5 mMsodium azide-41
Sample conditionsIonic strength: 0.113 / pH: 6.5 / 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
UNIOHerrmann and Wuthrichchemical shift assignment
UNIOHerrmann and Wuthrichstructure solution
UNIOHerrmann and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: OpalP
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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