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- PDB-5ghs: DNA replication protein -

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Basic information

Entry
Database: PDB / ID: 5ghs
TitleDNA replication protein
Components
  • Putative uncharacterized protein
  • SsDNA-specific exonuclease
KeywordsDNA BINDING PROTEIN/REPLICATION / DNA replication / DNA BINDING PROTEIN-REPLICATION complex
Function / homology
Function and homology information


exonuclease activity / nucleic acid binding
Similarity search - Function
Archaeal GINS complex, Gins51 subunit / Ribosomal Protein L9; domain 1 - #50 / : / DHH-CID domain / Ribosomal Protein L9; domain 1 / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain ...Archaeal GINS complex, Gins51 subunit / Ribosomal Protein L9; domain 1 - #50 / : / DHH-CID domain / Ribosomal Protein L9; domain 1 / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA replication complex GINS family protein / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.591 Å
AuthorsOyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS Japan
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication.
Authors: Oyama, T. / Ishino, S. / Shirai, T. / Yamagami, T. / Nagata, M. / Ogino, H. / Kusunoki, M. / Ishino, Y.
History
DepositionJun 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: SsDNA-specific exonuclease
B: SsDNA-specific exonuclease
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3179
Polymers123,8374
Non-polymers4805
Water79344
1
A: SsDNA-specific exonuclease
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2075
Polymers61,9182
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-40 kcal/mol
Surface area22680 Å2
MethodPISA
2
B: SsDNA-specific exonuclease
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1114
Polymers61,9182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-42 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.040, 116.277, 235.401
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 SsDNA-specific exonuclease


Mass: 52910.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1252 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5JGL0
#2: Protein Putative uncharacterized protein


Mass: 9008.398 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 131-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0536 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5JF31
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.591→50 Å / Num. obs: 42104 / % possible obs: 100 % / Redundancy: 7 % / Net I/σ(I): 18.6

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.591→44.478 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.84
RfactorNum. reflection% reflection
Rfree0.2729 2126 5.06 %
Rwork0.2373 --
obs0.2391 41983 99.6 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 17.768 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.9349 Å20 Å2-0 Å2
2--15.6275 Å20 Å2
3----2.7034 Å2
Refinement stepCycle: LAST / Resolution: 2.591→44.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7183 0 25 44 7252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037324
X-RAY DIFFRACTIONf_angle_d0.6869882
X-RAY DIFFRACTIONf_dihedral_angle_d14.772746
X-RAY DIFFRACTIONf_chiral_restr0.0521096
X-RAY DIFFRACTIONf_plane_restr0.0031295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5909-2.65110.37061610.31362491X-RAY DIFFRACTION95
2.6511-2.71740.34141430.31212594X-RAY DIFFRACTION100
2.7174-2.79090.32061310.28652636X-RAY DIFFRACTION100
2.7909-2.8730.32251310.28632614X-RAY DIFFRACTION100
2.873-2.96570.32871390.2662650X-RAY DIFFRACTION100
2.9657-3.07170.30341440.27632622X-RAY DIFFRACTION100
3.0717-3.19460.30161330.25672642X-RAY DIFFRACTION100
3.1946-3.340.31911540.25912614X-RAY DIFFRACTION100
3.34-3.5160.28861230.24652674X-RAY DIFFRACTION100
3.516-3.73620.26631390.23162654X-RAY DIFFRACTION100
3.7362-4.02450.26281310.21132700X-RAY DIFFRACTION100
4.0245-4.42910.24291530.19032652X-RAY DIFFRACTION100
4.4291-5.06930.21191560.18862683X-RAY DIFFRACTION100
5.0693-6.38370.22491340.23192753X-RAY DIFFRACTION100
6.3837-44.48440.23761540.22562878X-RAY DIFFRACTION99

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