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- PDB-1hh1: THE STRUCTURE OF HJC, A HOLLIDAY JUNCTION RESOLVING ENZYME FROM S... -

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Basic information

Entry
Database: PDB / ID: 1hh1
TitleTHE STRUCTURE OF HJC, A HOLLIDAY JUNCTION RESOLVING ENZYME FROM SULFOLOBUS SOLFATARICUS
ComponentsHOLLIDAY JUNCTION RESOLVING ENZYME HJC
KeywordsHOLLIDAY JUNCTION RESOLVASE / HOMOLOGOUS RECOMBINATION / NUCLEASE DOMAIN / ARCHAEA
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / 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 speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsBond, C.S. / Kvaratskhelia, M. / Richard, D. / White, M.F. / Hunter, W.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of Hjc, a Holliday Junction Resolvase, from Sulfolobus Solfataricus
Authors: Bond, C.S. / Kvaratskhelia, M. / Richard, D. / White, M.F. / Hunter, W.N.
History
DepositionDec 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOLLIDAY JUNCTION RESOLVING ENZYME HJC


Theoretical massNumber of molelcules
Total (without water)16,0401
Polymers16,0401
Non-polymers00
Water1,42379
1
A: HOLLIDAY JUNCTION RESOLVING ENZYME HJC

A: HOLLIDAY JUNCTION RESOLVING ENZYME HJC


Theoretical massNumber of molelcules
Total (without water)32,0802
Polymers32,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)52.699, 52.699, 207.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

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Components

#1: Protein HOLLIDAY JUNCTION RESOLVING ENZYME HJC


Mass: 16039.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UWX8, UniProt: Q7LXU0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 4.5
Details: 0.1M SODIUM ACETATE PH 4.5, 20% GLYCEROL, 20% PEG 4K, 0.16M AMMONIUM SULFATE
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG40001reservoir
20.08 Msodium acetate1reservoir
3160 mMammonium sulfate1reservoir
420 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97626
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 10061 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.041 / Net I/σ(I): 36
Reflection shellResolution: 2.15→2.2 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.105 / % possible all: 97
Reflection
*PLUS
Num. measured all: 121253 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.105

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.281 484 5 %RANDOM
Rwork0.22 ---
obs-10061 99.2 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 0 79 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2843
X-RAY DIFFRACTIONp_mcangle_it4.0435
X-RAY DIFFRACTIONp_scbond_it1.9626
X-RAY DIFFRACTIONp_scangle_it3.3768
X-RAY DIFFRACTIONp_plane_restr0.0519
X-RAY DIFFRACTIONp_chiral_restr0.0226
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35 Å2

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