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- PDB-7w8d: The structure of Deinococcus radiodurans RuvC -

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Basic information

Entry
Database: PDB / ID: 7w8d
TitleThe structure of Deinococcus radiodurans RuvC
ComponentsCrossover junction endodeoxyribonuclease RuvC
KeywordsHYDROLASE / holliday junction resolvase / DNase / DNA binding
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / DNA recombination / nucleic acid binding / DNA repair / magnesium ion binding
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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75016129042 Å
AuthorsCheng, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
CitationJournal: Mbio / Year: 2022
Title: Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans.
Authors: Sun, Y. / Yang, J. / Xu, G. / Cheng, K.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3883
Polymers39,3642
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-22 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.200, 72.770, 112.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: ruvC, DR_0440 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RX75, crossover junction endodeoxyribonuclease
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.2 M MgCl2, 0.1M HEPES (pH 7.8), 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→27.71 Å / Num. obs: 9594 / % possible obs: 91.2 % / Redundancy: 4 % / Biso Wilson estimate: 57.4767212532 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.4
Reflection shellResolution: 2.75→2.79 Å / Rmerge(I) obs: 0.722 / Num. unique obs: 674

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EP4

4ep4


Resolution: 2.75016129042→27.705522236 Å / SU ML: 0.400409488542 / Cross valid method: FREE R-VALUE / σ(F): 1.3549347961 / Phase error: 32.9446404357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.30581259884 434 5.2798053528 %
Rwork0.273390366557 7786 -
obs0.275071348481 8220 88.7976666307 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.2475739321 Å2
Refinement stepCycle: LAST / Resolution: 2.75016129042→27.705522236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 1 0 2348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004365751777742388
X-RAY DIFFRACTIONf_angle_d0.7573084139063231
X-RAY DIFFRACTIONf_chiral_restr0.045050258135374
X-RAY DIFFRACTIONf_plane_restr0.00387810933674414
X-RAY DIFFRACTIONf_dihedral_angle_d20.88076030121441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-3.14760.354207093031450.3291834929912613X-RAY DIFFRACTION91.5974759216
3.1476-3.96380.3009964978271490.3009843052622552X-RAY DIFFRACTION88.8486842105
3.9638-100.2943595734821400.2405680195482621X-RAY DIFFRACTION86.1197754211
Refinement TLS params.Method: refined / Origin x: 18.9841384343 Å / Origin y: 24.6401043917 Å / Origin z: 11.5409278192 Å
111213212223313233
T0.351284783604 Å20.00927308806243 Å2-0.0152024090477 Å2-0.44521585822 Å20.0615401103552 Å2--0.246525249017 Å2
L2.2959500313 °20.432664519325 °20.296987623653 °2-6.51778871726 °20.704667782685 °2--2.58287701216 °2
S-0.191369179879 Å °0.30636368511 Å °0.154183344965 Å °-0.848049081646 Å °-0.0270271277891 Å °-0.0487852236604 Å °-0.168455967225 Å °0.0282271498843 Å °0.220023430734 Å °
Refinement TLS groupSelection details: all

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