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- PDB-2k50: Solution NMR Structure of the replication Factor A Related Protei... -

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Basic information

Entry
Database: PDB / ID: 2k50
TitleSolution NMR Structure of the replication Factor A Related Protein from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Target TR91A.
ComponentsReplication factor A related protein
Keywordsstructural genomics / unknown function / uncharacterized protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA replication / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication factor A
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRossi, P. / Xiao, R. / Maglaqui, M. / Foote, E.L. / Ciccosanti, C. / Swapna, G. / Acton, T.B. / Rost, B. / Everett, J.K. / Jiang, M. ...Rossi, P. / Xiao, R. / Maglaqui, M. / Foote, E.L. / Ciccosanti, C. / Swapna, G. / Acton, T.B. / Rost, B. / Everett, J.K. / Jiang, M. / Nair, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the replication Factor A Related Protein from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Target TR91A.
Authors: Rossi, P. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication factor A related protein


Theoretical massNumber of molelcules
Total (without water)13,1701
Polymers13,1701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Replication factor A related protein


Mass: 13170.194 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Genus: Methanobacterium / Species: thermoautotrophicum
Description: experssion media: MJ9 100%N15 5%C13 and MJ9 100%N15 100%C13
Gene: MTH1385, MTH_1385 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O27438

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HNCO
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D CCH-TOCSY
11013D HBHA(CO)NH
11113D HN(CA)CO
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11422D 1H-15N HSQC
11522D 1H-13C HSQC
11622D HET NOE
1172Pseudo 2D T1
1182Pseudo 2D T2 (CPMG)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.33 mM U-100% 15N, 5 % 13C TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMTR91A[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMsodium chloride1
100 mMDTT1
5 mMCalcium Chloride1
0.02 %sodium azide1
1.33 mMTR91AU-100% 15N, 5 % 13C2
20 mMMES2
100 mMsodium chloride2
100 mMDTT2
5 mMCalcium Chloride2
0.02 %sodium azide2
Sample conditionsIonic strength: 0.1 / 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
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.113Goddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpin2.1Bruker Biospincollection
PSVSBhattacharya and Montelionevalidation
RPF(AutoStructure)Huang, Tejero, Powers and Montelionevalidation
MOLMOLKoradi, Billeter and Wuthrichvisualization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thovalidation
MolProbityRichardsonvalidation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: To be used for REMARK 210: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 842.8/71.47, TAUC = 10.6(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE ...Details: To be used for REMARK 210: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 842.8/71.47, TAUC = 10.6(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.53%, SIDECHAIN 88.01%, AROMATIC (SC) 95.83%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1945 NOE, 214 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 6.9 DEG. 2 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 8-36, 40-84, 91-104 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (18-28, 32-33, 43-51, 54-61, 76-84, 93-96, 102-105). RMSD 0.4 BACKBONE, 0.8 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 91.3/8.6/0.1/0.0. PROCHECK (PSI-PHI): -0.61/-2.08 (RAW/Z), PROCHECK (ALL): -0.33/-1.95 (RAW/Z), MOLPROBITY CLASH: 18.22/-1.60 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.93, PRECISION: 0.90, F-MEASURE: 0.92, DP-SCORE: 0.79.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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