- PDB-2pqa: Crystal Structure of Full-length Human RPA 14/32 Heterodimer -
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Basic information
Entry
Database: PDB / ID: 2pqa
Title
Crystal Structure of Full-length Human RPA 14/32 Heterodimer
Components
Replication protein A 14 kDa subunit
Replication protein A 32 kDa subunit
Keywords
REPLICATION / RPA14/32 / ssDNA binding protein / OB-fold
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 / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / 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
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor A protein-like / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor A protein-like / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta Similarity search - Domain/homology
A: Replication protein A 32 kDa subunit B: Replication protein A 14 kDa subunit C: Replication protein A 32 kDa subunit D: Replication protein A 14 kDa subunit
Resolution: 2.4→2.58 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3730 / Rsym value: 0.58 / % possible all: 97.3
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
SHELXS
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.578 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.551 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: High R value due to the disordered domain
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27981
1049
5.1 %
RANDOM
Rwork
0.22825
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obs
0.23091
19411
96.03 %
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all
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20156
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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: 37.724 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.69 Å2
0.84 Å2
0 Å2
2-
-
1.69 Å2
0 Å2
3-
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-2.53 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3785
0
0
0
3785
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
3850
X-RAY DIFFRACTION
r_angle_refined_deg
1.505
1.965
5220
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.534
5
477
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.374
24.847
163
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.503
15
687
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.583
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.113
0.2
617
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
2831
X-RAY DIFFRACTION
r_nbd_refined
0.23
0.2
1580
X-RAY DIFFRACTION
r_nbtor_refined
0.31
0.2
2595
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.146
0.2
111
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.192
0.2
47
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.197
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
0.71
1.5
2472
X-RAY DIFFRACTION
r_mcangle_it
1.238
2
3938
X-RAY DIFFRACTION
r_scbond_it
1.447
3
1526
X-RAY DIFFRACTION
r_scangle_it
2.291
4.5
1282
LS refinement shell
Resolution: 2.5→2.564 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.33
76
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Rwork
0.31
1428
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obs
-
1525
97.22 %
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