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- PDB-1jmc: SINGLE STRANDED DNA-BINDING DOMAIN OF HUMAN REPLICATION PROTEIN A... -

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Basic information

Entry
Database: PDB / ID: 1jmc
TitleSINGLE STRANDED DNA-BINDING DOMAIN OF HUMAN REPLICATION PROTEIN A BOUND TO SINGLE STRANDED DNA, RPA70 SUBUNIT, RESIDUES 183-420
Components
  • DNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • PROTEIN (REPLICATION PROTEIN A (RPA))
KeywordsREPLICATION/DNA / HUMAN SSDNA BINDING REPLICATION PROTEIN A(RPA) / SINGLE STRANDED DNA-BINDING PROTEIN / PROTEIN-SSDNA COMPLEX / COMPLEX (DNA-BINDING PROTEIN-DNA) / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / lateral element / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...protein localization to chromosome / DNA replication factor A complex / lateral element / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / HSF1 activation / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / 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 / meiotic cell cycle / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / PML body / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / 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 / chromosome, telomeric region / DNA replication / 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
DNA / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å
AuthorsBochkarev, A. / Pfuetzner, R. / Edwards, A. / Frappier, L.
Citation
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.
#1: 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
DepositionNov 11, 1996Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 16, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')
A: PROTEIN (REPLICATION PROTEIN A (RPA))


Theoretical massNumber of molelcules
Total (without water)29,7852
Polymers29,7852
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.250, 77.990, 95.360
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: DNA chain DNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 2268.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (REPLICATION PROTEIN A (RPA))


Mass: 27516.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P27694
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 40 %
Description: THREE DIFFERENT MONO-IODINATED AND ONE DI-IODINATED DNA DERIVATIVES WERE USED.
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8
Details: 24-27% PEG2000 MME, 20MM NA_CL, 20MM MGCL2, 5MM DTT, 100MM MES PH 6.8, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 200011
3NACL11
4MGCL211
5DTT11
6MES11
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124-27 %PEG2000 MME1reservoir
220 mM1reservoirNaCl
320 mM1reservoirMgCl2
45 mMDTT1reservoir
5100 mMBis-Tris1reservoir
6100 mM1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 25, 1996 / Details: MSC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 13045 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.2→2.34 Å / Rmerge(I) obs: 0.165 / % possible all: 87.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 35 Å / % possible obs: 95 % / Num. measured all: 141185
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASES(FUREY)phasing
X-PLORrefinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED INDIVIDUAL B F / σ(F): 2
Details: AMINO ACIDS 239 AND 259 ARE IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT.
RfactorNum. reflection% reflection
Rfree0.33 955 10 %
Rwork0.1 --
obs0.212 9460 95.5 %
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 169 0 270 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.4→2.5 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.357 116 -
Rwork0.257 1024 -
obs--93.4 %
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å

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