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- PDB-4ipg: Structure of the N-terminal domain of RPA70, E7R, E100R mutant -

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Basic information

Entry
Database: PDB / ID: 4ipg
TitleStructure of the N-terminal domain of RPA70, E7R, E100R mutant
ComponentsReplication protein A 70 kDa DNA-binding subunit
KeywordsPROTEIN BINDING / OB-fold
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / lateral element / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / protein localization to site of double-strand break / G-rich strand telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / chromatin-protein adaptor activity ...protein localization to chromosome / DNA replication factor A complex / lateral element / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / protein localization to site of double-strand break / G-rich strand telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / chromatin-protein adaptor activity / Removal of the Flap Intermediate from the C-strand / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / site of DNA damage / Activation of ATR in response to replication stress / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / mismatch repair / homeostasis of number of cells within a tissue / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / male germ cell nucleus / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / PML body / G2/M DNA damage checkpoint / base-excision repair / HDR through Homologous Recombination (HRR) / DNA-templated DNA replication / Meiotic recombination / Dual Incision in GG-NER / 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 / in utero embryonic development / damaged DNA binding / DNA replication / chromosome, telomeric region / DNA repair / positive regulation of cell population proliferation / DNA damage response / chromatin binding / zinc ion binding / nucleoplasm / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsFeldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Fesik, S.W. / Chazin, W.J.
CitationJournal: Biochemistry / Year: 2013
Title: Surface Reengineering of RPA70N Enables Cocrystallization with an Inhibitor of the Replication Protein A Interaction Motif of ATR Interacting Protein.
Authors: Feldkamp, M.D. / Frank, A.O. / Kennedy, J.P. / Patrone, J.D. / Vangamudi, B. / Waterson, A.G. / Fesik, S.W. / Chazin, W.J.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)13,5261
Polymers13,5261
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.490, 53.790, 54.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 13525.808 Da / Num. of mol.: 1 / Mutation: E7R, E100R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P27694
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Citrate, 200 mM NaCl, 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 22, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.58→24.266 Å / Num. obs: 16007 / % possible obs: 99.92 % / Observed criterion σ(F): 1.58 / Observed criterion σ(I): 1.58 / Redundancy: 5.9 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.065 / Net I/σ(I): 18.3
Reflection shellResolution: 1.58→1.6794 Å / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B29

2b29


Resolution: 1.58→24.266 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 799 4.99 %Random
Rwork0.1615 ---
all0.1634 ---
obs0.1634 16007 99.92 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→24.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 0 148 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181009
X-RAY DIFFRACTIONf_angle_d1.7961379
X-RAY DIFFRACTIONf_dihedral_angle_d13.721414
X-RAY DIFFRACTIONf_chiral_restr0.11167
X-RAY DIFFRACTIONf_plane_restr0.009179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5804-1.67940.23861230.19532499X-RAY DIFFRACTION100
1.6794-1.80910.2331350.1822478X-RAY DIFFRACTION100
1.8091-1.9910.22731320.15962506X-RAY DIFFRACTION100
1.991-2.2790.1981420.14642506X-RAY DIFFRACTION100
2.279-2.87050.20341320.16652554X-RAY DIFFRACTION100
2.8705-24.26890.18191350.15672665X-RAY DIFFRACTION100

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