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- PDB-7yik: The structure of archaeal nuclease RecJ2 from Methanocaldococcus ... -

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Basic information

Entry
Database: PDB / ID: 7yik
TitleThe structure of archaeal nuclease RecJ2 from Methanocaldococcus jannaschii
Componentsnuclease RecJ2
KeywordsDNA BINDING PROTEIN / nuclease RecJ2
Function / homology
Function and homology information


single-stranded DNA 5'-3' DNA exonuclease activity / DNA recombination / nucleic acid binding
Similarity search - Function
inorganic pyrophosphatase (n-terminal core) - #30 / : / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MJ0831
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.191 Å
AuthorsWang, W.W. / Liu, X.P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170097 China
National Natural Science Foundation of China (NSFC)U1832161 China
National Natural Science Foundation of China (NSFC)41921006 China
CitationJournal: To Be Published
Title: The structure of archaeal nuclease RecJ2 from Methanocaldococcus jannaschii
Authors: Wang, W.W. / Yi, G.S. / Zhou, H. / Zhao, Y.X. / Wang, Q.S. / He, J.H. / Yu, F. / Xiao, X. / Liu, X.P.
History
DepositionJul 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nuclease RecJ2
B: nuclease RecJ2


Theoretical massNumber of molelcules
Total (without water)97,8122
Polymers97,8122
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-19 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.522, 177.818, 66.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein nuclease RecJ2


Mass: 48905.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: MJ0831 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58241
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 400, 50mM HEPES pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→29.64 Å / Num. obs: 99462 / % possible obs: 99.1 % / Redundancy: 14.1 % / Biso Wilson estimate: 39.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.089 / Net I/σ(I): 22.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.19-2.2513.90.7944881735040.8790.2170.8233.490.9
9.8-29.6410.80.03568496330.9990.0110.03751.892.8

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.191→29.636 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 3796 3.82 %
Rwork0.1954 95666 -
obs0.1974 99462 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.98 Å2 / Biso mean: 49.319 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.191→29.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6827 0 0 229 7056
Biso mean---47.09 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086947
X-RAY DIFFRACTIONf_angle_d0.8799349
X-RAY DIFFRACTIONf_chiral_restr0.0521057
X-RAY DIFFRACTIONf_plane_restr0.0051185
X-RAY DIFFRACTIONf_dihedral_angle_d3.2384215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1914-2.21910.31491170.2675293183
2.2191-2.24830.27631430.25173595100
2.2483-2.27910.32541430.25143562100
2.2791-2.31160.31731410.2568355199
2.3116-2.34610.30961390.23833536100
2.3461-2.38280.31611420.2358360199
2.3828-2.42180.29191380.23923537100
2.4218-2.46360.29621420.2282359599
2.4636-2.50830.32951430.23293555100
2.5083-2.55650.29041400.2243518100
2.5565-2.60870.31571440.22093571100
2.6087-2.66540.27611410.21143602100
2.6654-2.72730.27281400.20333537100
2.7273-2.79550.29791440.20833567100
2.7955-2.8710.23261440.21933611100
2.871-2.95540.27871460.21033543100
2.9554-3.05070.27421370.21683570100
3.0507-3.15970.27951450.21283624100
3.1597-3.2860.28071410.21383562100
3.286-3.43530.28491390.20773521100
3.4353-3.61620.251390.1993570100
3.6162-3.84230.24471430.18633611100
3.8423-4.13820.20711430.17523577100
4.1382-4.55330.21461460.16043530100
4.5533-5.20910.16991430.16693584100
5.2091-6.55120.27631370.1983603100
6.5512-29.6360.1981360.149350298

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