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

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Basic information

Entry
Database: PDB / ID: 4ipc
TitleStructure of the N-terminal domain of RPA70, E7R 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 / chromatin-protein adaptor activity / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / protein localization to site of double-strand break / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding ...protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / protein localization to site of double-strand break / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / 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 / HSF1 activation / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / mismatch repair / 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 / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / base-excision repair / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / PML body / Dual Incision in GG-NER / DNA-templated DNA replication / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / site of double-strand break / single-stranded DNA binding / 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 / nucleus / metal ion binding
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: 1.22 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)13,4981
Polymers13,4981
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.540, 53.720, 54.360
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: 13497.728 Da / Num. of mol.: 1 / Mutation: E7R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / 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.: 123 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, 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: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.22→31.44 Å / Num. obs: 34199 / % possible obs: 99.72 % / Observed criterion σ(F): 1.22 / Observed criterion σ(I): 1.22 / Redundancy: 5.9 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 15.37

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B29

2b29


Resolution: 1.22→31.44 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 1732 5.06 %Random
Rwork0.1459 ---
obs0.1474 34198 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 123 1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091080
X-RAY DIFFRACTIONf_angle_d1.4061490
X-RAY DIFFRACTIONf_dihedral_angle_d12.19447
X-RAY DIFFRACTIONf_chiral_restr0.085182
X-RAY DIFFRACTIONf_plane_restr0.006195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.25590.25351470.20032664X-RAY DIFFRACTION100
1.2559-1.29640.20511380.17282685X-RAY DIFFRACTION100
1.2964-1.34280.2191310.15332686X-RAY DIFFRACTION100
1.3428-1.39650.17751410.13152664X-RAY DIFFRACTION100
1.3965-1.46010.16691390.12682676X-RAY DIFFRACTION100
1.4601-1.53710.15011400.12082707X-RAY DIFFRACTION100
1.5371-1.63340.16491410.11492677X-RAY DIFFRACTION100
1.6334-1.75950.16091390.12032718X-RAY DIFFRACTION100
1.7595-1.93650.15631640.13112695X-RAY DIFFRACTION100
1.9365-2.21670.14021340.122730X-RAY DIFFRACTION100
2.2167-2.79250.1641730.15242739X-RAY DIFFRACTION100
2.7925-31.45050.20471450.16842825X-RAY DIFFRACTION97

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