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- PDB-2k5v: SOLUTION NMR STRUCTURE OF the second OB-fold domain of replicatio... -

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Basic information

Entry
Database: PDB / ID: 2k5v
TitleSOLUTION NMR STRUCTURE OF the second OB-fold domain of replication protein A from Methanococcus maripaludis. NORTHEAST STRUCTURAL GENOMICS TARGET MrR110B.
ComponentsReplication protein ADNA replication
KeywordsDNA BINDING PROTEIN / solution NMR structure / replication protein A / OB-fold domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyOB-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 / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Replication protein A
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Maglaqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.VT. / Acton, T.B. / Rost, B. ...Aramini, J.M. / Maglaqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.VT. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: SOLUTION NMR STRUCTURE OF the second OB-fold domain of replication protein A from Methanococcus maripaludis. NORTHEAST STRUCTURAL GENOMICS TARGET MrR110B.
Authors: Aramini, J.M. / Maglaqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.VT. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A


Theoretical massNumber of molelcules
Total (without water)11,6311
Polymers11,6311
Non-polymers00
Water0
1


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

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Components

#1: Protein Replication protein A / DNA replication


Mass: 11631.123 Da / Num. of mol.: 1 / Mutation: T193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Species: maripaludis / Gene: rpa, MMP1032 / Plasmid: MrR110B-21.1 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q6LYF9

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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 HNCO
1413D HN(CA)CO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-COSY ALIPHATIC
1913D (H)CCH-TOCSY ALIPHATIC
11013D CCH-TOCSY ALIPHATIC
11113D HNHA
11213D SIMULTANEOUS CN NOESY
11313D 1H-13C NOESY aromatic
11412D 1H-13C HSQC HIGH RES. (L/V STEREOASSIGNMENT)
11512D 1H-15N HETNOE
11612D 1H-15N T1/T2
NMR detailsText: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. BACKBONE (PHI/ PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C- TERMINAL HHHHHH): BACKBONE, 100%, SIDE CHAIN, 99.7%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 172 TO 269, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 173-204,209-249,254-265: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 92.4%, ADDITIONALLY ALLOWED, 6.6%, GENEROUSLY ALLOWED, 1.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.60/-2.05, ALL, -0.36/-2.13. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 16.29/-1.27 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 172-269): RECALL, 0.990, PRECISION, 0.933, F-MEASURE, 0.961, DP-SCORE, 0.836. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 172,205-208,250-253, 266-269.

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Sample preparation

DetailsContents: 1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM ...Contents: 1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.18 mMMrR110B[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
1.18 mMMrR110B[U-100% 13C; U-100% 15N]2
20 mMMES2
100 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
0.94 mMMrR110B[U-5% 13C; U-100% 15N]3
20 mMMES3
100 mMsodium chloride3
5 mMcalcium chloride3
10 mMDTT3
0.02 %sodium azide3
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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER, ADAMS, CLORE, GROS, NILGESrefinement
TopSpin2.1structure solution
AutoAssign2.4.0structure solution
NMRPipe2.3structure solution
CYANA2.1structure solution
CNS1.2structure solution
Sparky3.113structure solution
AutoStructure2.2.1structure solution
PSVS1.3structure solution
PdbStat5structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1692 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1692 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 CONSTRAINTS PER RESIDUE, 6.2 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 172 TO 269 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.
NMR constraintsNOE constraints total: 1692 / NOE intraresidue total count: 477 / NOE long range total count: 612 / NOE medium range total count: 170 / NOE sequential total count: 433 / Protein chi angle constraints total count: 4 / Protein other angle constraints total count: 4 / Protein phi angle constraints total count: 58 / Protein psi angle constraints total count: 59
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.01 Å

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