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- PDB-2m7o: NMR Structure of the protein NP_346341.1 from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 2m7o
TitleNMR Structure of the protein NP_346341.1 from Streptococcus pneumoniae
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homologyUncharacterised protein PF15513, DUF4651 / Protein of unknown function DUF4651 / Domain of unknown function (DUF4651) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4651 domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model5
AuthorsProudfoot, A. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR Structure of the protein NP_346341.1 from Streptococcus pneumoniae
Authors: Proudfoot, A. / Wuthrich, K.
History
DepositionApr 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: 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
Revision 1.3May 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)8,1881
Polymers8,1881
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: 8187.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1912 / Plasmid: Pspeedet / Production host: Escherichia coli (E. coli) / References: UniProt: Q97NU9, UniProt: A0A0H2URM0*PLUS

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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: 0.22 / 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichcollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichcollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichcollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichcollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichcollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
OPALprefinement
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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