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- PDB-2b29: N-terminal domain of the RPA70 subunit of human replication protein A. -

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Basic information

Entry
Database: PDB / ID: 2b29
TitleN-terminal domain of the RPA70 subunit of human replication protein A.
ComponentsReplication protein A 70 kDa DNA-binding subunitDNA replication
KeywordsREPLICATION
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / single-stranded telomeric DNA binding / Removal of the Flap Intermediate from the C-strand ...protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / single-stranded telomeric DNA binding / Removal of the Flap Intermediate from the C-strand / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / 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 ...Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / 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 protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 Å
AuthorsBochkareva, E. / Kaustov, L. / Ayed, A. / Okorokov, A. / Milner, J. / Arrowsmith, C.H. / Bochkarev, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A.
Authors: Bochkareva, E. / Kaustov, L. / Ayed, A. / Yi, G.S. / Lu, Y. / Pineda-Lucena, A. / Liao, J.C. / Okorokov, A.L. / Milner, J. / Arrowsmith, C.H. / Bochkarev, A.
History
DepositionSep 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit


Theoretical massNumber of molelcules
Total (without water)13,4701
Polymers13,4701
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.692, 57.692, 63.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / DNA replication / RP-A / RF-A / Replication factor-A protein 1 / Single-stranded DNA-binding protein


Mass: 13469.647 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 1-120)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Plasmid: pET15B-RPA70N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27694
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium Sulphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 2003
RadiationMonochromator: Rigaku/MSC Confocal Multilyer Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 15911 / Num. obs: 15899 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR
Starting model: None

Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.252 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 794 5 %RANDOM
Rwork0.21829 ---
all0.22036 15073 --
obs0.22036 15073 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.101 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 0 114 1015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9961236
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17825.27836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29115170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.841156
X-RAY DIFFRACTIONr_chiral_restr0.1410.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02662
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.2441
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2638
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5991.5604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3592959
X-RAY DIFFRACTIONr_scbond_it3.053334
X-RAY DIFFRACTIONr_scangle_it4.5754.5277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 59 -
Rwork0.421 1101 -
obs--100 %

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