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- PDB-1ipi: CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC... -

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Basic information

Entry
Database: PDB / ID: 1ipi
TitleCRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM II
ComponentsHOLLIDAY JUNCTION RESOLVASE
KeywordsHYDROLASE / nuclease fold / HJC
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
Similarity search - Function
Holliday junction resolvase Hjc / Holliday junction resolvase Hjc, archaeal / Archaeal holliday junction resolvase (hjc) / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Crossover junction endodeoxyribonuclease Hjc / Crossover junction endodeoxyribonuclease Hjc
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsNishino, T. / Komori, K. / Ishino, Y. / Morikawa, K.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses.
Authors: Nishino, T. / Komori, K. / Ishino, Y. / Morikawa, K.
History
DepositionMay 15, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: HOLLIDAY JUNCTION RESOLVASE
B: HOLLIDAY JUNCTION RESOLVASE


Theoretical massNumber of molelcules
Total (without water)27,5852
Polymers27,5852
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-14 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.969, 59.969, 134.554
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Detailschain A and B form functional dimer

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Components

#1: Protein HOLLIDAY JUNCTION RESOLVASE / HJC


Mass: 13792.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: HJC / Plasmid: PET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V301, UniProt: E7FHX4*PLUS, crossover junction endodeoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7
Details: 100mM Tris-HCl, 1mM EDTA, 32.5% PEG4000, 10% glycerol , pH 7.0, VAPOR DIFFUSION, temperature 297K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
2100 mMTris-HCl11pH7.0
31 mMEDTA11
432.5 %(w/v)PEG400011
510 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 11, 2000
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 2.15→41.1 Å / Num. all: 94745 / Num. obs: 13043 / % possible obs: 88.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.42
Reflection shellResolution: 2.16→2.26 Å / Redundancy: 6 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.7 / % possible all: 79.5
Reflection
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 41 Å / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Lowest resolution: 2.27 Å / % possible obs: 79.5 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GEF functional dimer

1gef


Resolution: 2.16→41 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1334 11.48 %RANDOM
Rwork0.214 ---
all-12955 --
obs-11621 --
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.16→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 0 157 1959
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d23.8463
X-RAY DIFFRACTIONc_angle_d1.31928
X-RAY DIFFRACTIONc_bond_d0.006197
X-RAY DIFFRACTIONc_improper_angle_d0.61779
LS refinement shellResolution: 2.16→2.24 Å
RfactorNum. reflection% reflection
Rfree0.307 120 -
Rwork0.233 --
obs-1035 0.784 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 41 Å / Num. reflection obs: 13043 / % reflection Rfree: 11.48 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8463
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.61779
LS refinement shell
*PLUS
Lowest resolution: 2.27 Å / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.233 / Rfactor obs: 0.233

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