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- PDB-2ml5: NMR structure of protein ZP_02064002.1 from Bacteroides ovatus AT... -

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Basic information

Entry
Database: PDB / ID: 2ml5
TitleNMR structure of protein ZP_02064002.1 from Bacteroides ovatus ATCC 8483
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / gut microbiome secreted protein / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homologyNuclear Transport Factor 2; Chain: A, - #410 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model5
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of protein ZP_02064002.1 from Bacteroides ovatus ATCC 8483
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionFeb 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references / Structure summary
Revision 1.2Feb 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 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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)17,9631
Polymers17,9631
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


Mass: 17962.908 Da / Num. of mol.: 1 / Fragment: UNP residues 33-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_00961 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: A7LT22

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111APSY 4D-HACANH
121APSY 5D-(HA)CA(CO)NH
131APSY 5D-CBCA(CO)NH
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1813D HNCA

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 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-99% 13C; U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMsodium azide-41
Sample conditionsIonic strength: 0.0798 / pH: 6 / Pressure: ambient / Temperature: 308 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 P.structure solution
CYANAGuntert P.chemical shift assignment
CYANAGuntert P.peak picking
j-UNIOHerrmann and Wuthrichstructure solution
j-UNIOHerrmann and Wuthrichchemical shift assignment
j-UNIOHerrmann and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichgeometry optimization
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
PROSAGuntertprocessing
GAPROHiller Speak picking
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2230 / NOE intraresidue total count: 618 / NOE long range total count: 637 / NOE medium range total count: 377 / NOE sequential total count: 598
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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