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- PDB-5ghr: DNA replication protein -

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Basic information

Entry
Database: PDB / ID: 5ghr
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 / SAD / Resolution: 2.509 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 1.1Dec 6, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SsDNA-specific exonuclease
B: Putative uncharacterized protein
C: SsDNA-specific exonuclease
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,8189
Polymers125,3374
Non-polymers4805
Water1,08160
1
A: SsDNA-specific exonuclease
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9575
Polymers62,6692
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-34 kcal/mol
Surface area22510 Å2
MethodPISA
2
C: SsDNA-specific exonuclease
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8614
Polymers62,6692
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-50 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.097, 116.004, 234.597
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: 53425.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (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: 9242.874 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


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


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 298 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-NW12A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 45946 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.509→25.038 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 26.64
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2488 4322 5.08 %
Rwork0.212 --
obs0.2139 45946 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.509→25.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7089 0 25 60 7174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027227
X-RAY DIFFRACTIONf_angle_d0.5059753
X-RAY DIFFRACTIONf_dihedral_angle_d12.2072719
X-RAY DIFFRACTIONf_chiral_restr0.021087
X-RAY DIFFRACTIONf_plane_restr0.0021276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5094-2.53790.37081240.27572162X-RAY DIFFRACTION80
2.5379-2.56770.3021270.26852481X-RAY DIFFRACTION91
2.5677-2.5990.34361580.26212553X-RAY DIFFRACTION94
2.599-2.63190.31441400.25112610X-RAY DIFFRACTION95
2.6319-2.66650.35171390.26052689X-RAY DIFFRACTION96
2.6665-2.7030.28861330.25442578X-RAY DIFFRACTION96
2.703-2.74150.27911260.24482689X-RAY DIFFRACTION98
2.7415-2.78240.28631510.24712749X-RAY DIFFRACTION99
2.7824-2.82580.31151760.25052701X-RAY DIFFRACTION99
2.8258-2.87210.33321240.25882716X-RAY DIFFRACTION99
2.8721-2.92150.28391800.24782682X-RAY DIFFRACTION100
2.9215-2.97460.27931550.24362768X-RAY DIFFRACTION100
2.9746-3.03170.32821260.25272747X-RAY DIFFRACTION99
3.0317-3.09350.25261510.25152711X-RAY DIFFRACTION100
3.0935-3.16060.28791610.23362728X-RAY DIFFRACTION100
3.1606-3.2340.30451320.2292766X-RAY DIFFRACTION100
3.234-3.31470.31811540.23892708X-RAY DIFFRACTION100
3.3147-3.40410.2981290.22332800X-RAY DIFFRACTION100
3.4041-3.5040.24871560.21952709X-RAY DIFFRACTION100
3.504-3.61680.27461250.20372745X-RAY DIFFRACTION100
3.6168-3.74560.18651490.19672780X-RAY DIFFRACTION100
3.7456-3.89510.18991650.18592668X-RAY DIFFRACTION100
3.8951-4.07160.19391250.17452778X-RAY DIFFRACTION100
4.0716-4.28530.19271440.17272757X-RAY DIFFRACTION100
4.2853-4.55230.20331700.17242674X-RAY DIFFRACTION100
4.5523-4.90140.21491610.17312777X-RAY DIFFRACTION100
4.9014-5.39020.18061290.19192761X-RAY DIFFRACTION100
5.3902-6.160.22191230.21472741X-RAY DIFFRACTION100
6.16-7.72290.23551410.19852754X-RAY DIFFRACTION100
7.7229-25.03910.2341480.18962729X-RAY DIFFRACTION99

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