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- PDB-1fgu: SSDNA-BINDING DOMAIN OF THE LARGE SUBUNIT OF REPLICATION PROTEIN A -

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Basic information

Entry
Database: PDB / ID: 1fgu
TitleSSDNA-BINDING DOMAIN OF THE LARGE SUBUNIT OF REPLICATION PROTEIN A
ComponentsREPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT
KeywordsREPLICATION / OB-fold / ssDNA-binding protein
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / protein localization to site of double-strand break / 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 ...protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / protein localization to site of double-strand break / 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 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / 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 / 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 / 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 / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / damaged DNA binding / 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 / MAD / Resolution: 2.5 Å
AuthorsBochkareva, E. / Belegu, V. / Korolev, S. / Bochkarev, A.
Citation
Journal: EMBO J. / Year: 2001
Title: Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding.
Authors: Bochkareva, E. / Belegu, V. / Korolev, S. / Bochkarev, A.
#1: Journal: Nature / Year: 1997
Title: Structure of the Single-stranded-DNA-binding Domain of Replication Protein A Bound to DNA
Authors: Bochkarev, A. / Pfuetzner, R.A. / Edwards, A.M. / Frappier, L.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Replication Protein A: Characterization and Crystallization of the DNA-binding Domain
Authors: Pfuetzner, R.A. / Bochkarev, A. / Frappier, L. / Edwards, A.M.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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
B: REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT


Theoretical massNumber of molelcules
Total (without water)56,2192
Polymers56,2192
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.500, 84.860, 119.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a trimer of 70, 32, and 14 kDa subunit THE BIOLOGICAL ASSEMBLY IS A TRIMER OF 70, 32, and 14 KDA SUBUNITS

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Components

#1: Protein REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT / SINGLE-STRANDED DNA-BINDING PROTEIN / REPLICATION FACTOR-A PROTEIN 1 / RF-A / RP-A


Mass: 28109.641 Da / Num. of mol.: 2 / Fragment: CENTRAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P27694
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M K,NaH2PO4 0.1 M Tris 3.8 M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-10 mg/mlprotein1drop
215 mMHEPES1drop
3350 mM1dropNaCl
45 mMdithiothreitol1drop
50.1 Msodium potassium phospahte1reservoir
60.1 MTris1reservoir
73.8 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: SBC-2 / Detector: CCD / Date: Jan 27, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 247836 / Num. obs: 22963 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 37.1
Reflection shellResolution: 2.49→2.58 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2191 / % possible all: 96
Reflection
*PLUS
Num. measured all: 247836
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
PHASESphasing
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 1.5 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: CRYSTALS DIFFRACTED ANYSOTROPICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1771 10 %RANDOM
Rwork0.215 ---
obs0.215 19729 86.2 %-
all-22875 --
Solvent computationSolvent model: CNS DEFAULT BULK SOLVENT / Bsol: 39.1 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 56.99 Å2
Baniso -1Baniso -2Baniso -3
1--14.4 Å20 Å20 Å2
2---3.8 Å20 Å2
3---18.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 0 32 3827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_torsion_deg25.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.75
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.32.5
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scbond_it3.63
X-RAY DIFFRACTIONc_scangle_it4.33.5
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
Num. reflection% reflection
Rfree99 4.4 %
Rwork1360 -
obs-64.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.75
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
X-RAY DIFFRACTIONc_mcbond_it2.32.5
X-RAY DIFFRACTIONc_scbond_it3.63
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scangle_it4.33.5
LS refinement shell
*PLUS
% reflection Rfree: 4.4 %

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