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- PDB-2kzf: Solution NMR structure of the thermotoga maritima protein TM0855 ... -

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Basic information

Entry
Database: PDB / ID: 2kzf
TitleSolution NMR structure of the thermotoga maritima protein TM0855 a putative ribosome binding factor A
ComponentsRibosome-binding factor A
KeywordsRIBOSOMAL PROTEIN / JCSG / Joint Center Structural Genomics / Protein Structure Initiative / Joint Center for Structural Genomics / PSI
Function / homology
Function and homology information


ribosomal small subunit binding / maturation of SSU-rRNA / ribosome biogenesis / cytosol
Similarity search - Function
Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding factor A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsSerrano, P. / Jaudzems, K. / Horst, R. / Wilson, I.A. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Solution NMR structure of the thermotoga maritima protein TM0855
Authors: Serrano, P. / Jaudzems, K. / Horst, R. / Wilson, I.A. / Wuthrich, K.
History
DepositionJun 16, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3Mar 20, 2013Group: Other
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)12,5031
Polymers12,5031
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 Ribosome-binding factor A / RbfA


Mass: 12502.525 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rbfA, TM_0855 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZV9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of the thermotoga maritima protein TM0855
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-13C NOESY (ali)
1413D 1H-13C NOESY (aro)
1513D 1H-15N NOESY
1614D APSY-HACANH
1715D APSY-(HA)CA(CO)NH
1815D APSY-CBCA(CO)NH

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Sample preparation

DetailsContents: 1.2 mM TM0855, 5 mM sodium azide, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.2 mMTM0855-11
5 mMsodium azide-21
20 mMsodium phosphate-31
50 mMsodium chloride-41
Sample conditionsIonic strength: 0.12 / pH: 6.5 / 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
CYANA3G ntert P.refinement
UNIOHerrmann and Wuthrichchemical shift assignment
UNIOHerrmann and Wuthrichstructure solution
OPALOpalpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle 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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