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

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Basic information

Entry
Database: PDB / ID: 7ykv
TitleThe structure of archaeal nuclease RecJ2 from Methanocaldococcus jannaschii
Componentsarchaeal nuclease 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 / Hydrolases; Acting on ester bonds
Similarity search - Function
inorganic pyrophosphatase (n-terminal core) - #30 / : / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 ...inorganic pyrophosphatase (n-terminal core) - #30 / : / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-IXK / Exonuclease RecJ2
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 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 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 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

Downloads & links

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Assembly

Deposited unit
A: archaeal nuclease RecJ2
B: archaeal nuclease RecJ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,31511
Polymers98,1422
Non-polymers1,1739
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-6 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.481, 175.395, 66.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein archaeal nuclease RecJ2


Mass: 49071.094 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: Chemical ChemComp-IXK / [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)furan-3-yl] [5-(6-aminopurin-9-yl)-3-oxidanyl-furan-2-yl]methyl hydrogen phosphate


Mass: 556.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N10O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% 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: 0.9791 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.04→175.4 Å / Num. obs: 62817 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.058 / Rrim(I) all: 0.158 / Net I/σ(I): 12.1 / Num. measured all: 456615
Reflection shellResolution: 2.04→2.09 Å / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 1.105 / Num. measured all: 33745 / Num. unique obs: 4576 / CC1/2: 0.741 / Rpim(I) all: 0.434 / Rrim(I) all: 1.189 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→75.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.629 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22557 3057 4.9 %RANDOM
Rwork0.17094 ---
obs0.17353 59694 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---1.1 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.04→75.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 79 543 7486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166863
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.6369576
X-RAY DIFFRACTIONr_angle_other_deg0.481.56415987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.881027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.475101354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6573.1023472
X-RAY DIFFRACTIONr_mcbond_other2.6573.1023472
X-RAY DIFFRACTIONr_mcangle_it3.8024.6394341
X-RAY DIFFRACTIONr_mcangle_other3.8014.644342
X-RAY DIFFRACTIONr_scbond_it3.7913.6853639
X-RAY DIFFRACTIONr_scbond_other3.7913.6853640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.865.2955227
X-RAY DIFFRACTIONr_long_range_B_refined7.41741.18167
X-RAY DIFFRACTIONr_long_range_B_other7.36839.6768040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 221 -
Rwork0.259 4347 -
obs--99.91 %

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