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- PDB-5ght: DNA replication protein -

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Basic information

Entry
Database: PDB / ID: 5ght
TitleDNA replication protein
ComponentsSsDNA-specific exonuclease
KeywordsDNA BINDING PROTEIN / DNA replication
Function / homology
Function and homology information


exonuclease activity / nucleic acid binding
Similarity search - Function
: / DHH-CID domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SsDNA-specific exonuclease


Theoretical massNumber of molelcules
Total (without water)52,9101
Polymers52,9101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.133, 158.133, 158.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein SsDNA-specific exonuclease


Mass: 52910.023 Da / Num. of mol.: 1
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

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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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.795→50 Å / Num. obs: 16452 / % possible obs: 99.9 % / Redundancy: 13.7 % / Net I/σ(I): 45

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GHR

5ghr


Resolution: 2.795→42.263 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.16
RfactorNum. reflection% reflection
Rfree0.2507 831 5.06 %
Rwork0.203 --
obs0.2054 16423 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.795→42.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 0 0 3630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033691
X-RAY DIFFRACTIONf_angle_d0.6684976
X-RAY DIFFRACTIONf_dihedral_angle_d13.7421386
X-RAY DIFFRACTIONf_chiral_restr0.027550
X-RAY DIFFRACTIONf_plane_restr0.003656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7954-2.97050.32781570.25772564X-RAY DIFFRACTION100
2.9705-3.19980.34311440.26522542X-RAY DIFFRACTION100
3.1998-3.52170.33391140.22842605X-RAY DIFFRACTION100
3.5217-4.03090.27491460.20662581X-RAY DIFFRACTION100
4.0309-5.07720.18651370.17862609X-RAY DIFFRACTION100
5.0772-42.26760.19821330.17542691X-RAY DIFFRACTION100

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