+Open data
-Basic information
Entry | Database: PDB / ID: 2pi2 | ||||||
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Title | Full-length Replication protein A subunits RPA14 and RPA32 | ||||||
Components |
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Keywords | REPLICATION / DNA BINDING PROTEIN / full-length RPA14/32 / ssDNA binding protein / OB-fold / Dioxane | ||||||
Function / homology | Function and homology information protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 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 ...protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 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 / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / mismatch repair / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / 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 / 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 / site of double-strand break / single-stranded DNA binding / regulation of cell population proliferation / Processing of DNA double-strand break ends / protein phosphatase binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / ubiquitin protein ligase binding / chromatin / enzyme binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Deng, X. / Borgstahl, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure of the Full-length Human RPA14/32 Complex Gives Insights into the Mechanism of DNA Binding and Complex Formation. Authors: Deng, X. / Habel, J.E. / Kabaleeswaran, V. / Snell, E.H. / Wold, M.S. / Borgstahl, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pi2.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pi2.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pi2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pi2_validation.pdf.gz | 517.8 KB | Display | wwPDB validaton report |
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Full document | 2pi2_full_validation.pdf.gz | 537.8 KB | Display | |
Data in XML | 2pi2_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2pi2_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/2pi2 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/2pi2 | HTTPS FTP |
-Related structure data
Related structure data | 2pqaC 2z6kC 1quqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29276.795 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPA2, REPA2, RPA32 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P15927 #2: Protein | Mass: 16117.456 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPA3, REPA3, RPA14 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P35244 #3: Chemical | ChemComp-DIO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% dioxane, 0.1 M MES pH 6.5, 39% saturated ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 170250 / Num. obs: 162767 / % possible obs: 95 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 98.59 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUQ Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.585 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.137 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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