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- PDB-7xhj: Crystal structure of RuvC from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7xhj
TitleCrystal structure of RuvC from Deinococcus radiodurans
ComponentsCrossover junction endodeoxyribonuclease RuvC
KeywordsDNA BINDING PROTEIN / nuclease / DNA repair / Homologous recombination / Holliday junction resolvase
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Crossover junction endodeoxyribonuclease RuvC / Crossover junction endodeoxyribonuclease RuvC / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Crossover junction endodeoxyribonuclease RuvC
Similarity search - Component
Biological speciesDeinococcus radiodurans ATCC 13939 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsQin, C. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503900) China
CitationJournal: Microorganisms / Year: 2022
Title: Structural and Functional Characterization of the Holliday Junction Resolvase RuvC from Deinococcus radiodurans.
Authors: Qin, C. / Han, W. / Xu, Y. / Zhao, Y. / Xu, H. / Tian, B. / Wang, L. / Hua, Y.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crossover junction endodeoxyribonuclease RuvC
B: Crossover junction endodeoxyribonuclease RuvC


Theoretical massNumber of molelcules
Total (without water)39,3642
Polymers39,3642
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-17 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.020, 72.600, 113.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Crossover junction endodeoxyribonuclease RuvC / Holliday junction nuclease RuvC / Holliday junction resolvase RuvC


Mass: 19681.842 Da / Num. of mol.: 2 / Fragment: Catalytic core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans ATCC 13939 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: ruvC, DR_0440 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9RX75, crossover junction endodeoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: ammonium sulfate, BIS-TRIS, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→27.54 Å / Num. obs: 42426 / % possible obs: 94.7 % / Redundancy: 3.772 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.057 / Χ2: 1.025 / Net I/σ(I): 16.52 / Num. measured all: 160024 / Scaling rejects: 185
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.643.8690.3554.3512078322531220.9210.41196.8
1.64-1.694.0140.2935.3212760318231790.9390.33899.9
1.69-1.733.8970.2446.4812038310930890.9460.28299.4
1.73-1.794.0230.1837.6811990298429800.9720.2199.9
1.79-1.854.0350.1479.2211819293229290.9810.16999.9
1.85-1.913.6810.12911.029972284027090.9820.15195.4
1.91-1.983.6150.09613.999240273025560.9870.11393.6
1.98-2.063.8540.07116.59709261025190.9930.08296.5
2.06-2.163.7460.0619.159148252824420.9950.0796.6
2.16-2.263.6730.05721.188419243222920.9940.06694.2
2.26-2.383.8710.04523.348881230922940.9980.05199.4
2.38-2.533.9090.0425.548557220521890.9970.04699.3
2.53-2.73.7720.0426.647567206620060.9980.04697.1
2.7-2.923.8690.03828.797336192418960.9980.04398.5
2.92-3.23.7790.03329.826701179917730.9980.03898.6
3.2-3.583.4640.03329.945404162715600.9970.03895.9
3.58-4.132.9580.03128.363623144212250.9970.03785
4.13-5.062.8340.02927.69236612538350.9970.03566.6
5.06-7.152.9660.02828.2420269896830.9980.03369.1
7.15-27.542.6350.02725.23906001480.9980.03324.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HJR

1hjr


Resolution: 1.6→27.54 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 2085 4.92 %
Rwork0.2045 40284 -
obs0.2054 42369 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.92 Å2 / Biso mean: 31.6299 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: final / Resolution: 1.6→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 0 151 2378
Biso mean---42.54 -
Num. residues----303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.22391220.21572694281697
1.64-1.680.22251490.211427822931100
1.68-1.720.26851510.21552765291699
1.72-1.770.22651440.208627822926100
1.77-1.830.24371490.206828152964100
1.83-1.90.25681290.20822737286698
1.9-1.970.28791320.24822565269792
1.97-2.060.1921570.19532708286598
2.06-2.170.25061220.20062738286096
2.17-2.310.22551460.20622694284095
2.31-2.480.21061400.18762822296299
2.48-2.730.20021560.18642762291898
2.73-3.130.18681440.19052848299299
3.13-3.940.1981500.18632690284093
3.94-27.540.2855940.25391882197662
Refinement TLS params.Method: refined / Origin x: 17.9966 Å / Origin y: -10.5586 Å / Origin z: 12.2749 Å
111213212223313233
T0.1354 Å20.0162 Å2-0.0146 Å2-0.1747 Å2-0.0061 Å2--0.1226 Å2
L0.3321 °2-0.1854 °20.0951 °2-2.5521 °20.0955 °2--0.4478 °2
S0.0024 Å °0.0428 Å °0.0029 Å °-0.2489 Å °-0.0245 Å °0.0458 Å °-0.019 Å °0.0191 Å °0.0006 Å °
Refinement TLS groupSelection details: all

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