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- PDB-1ob8: Holliday Junction Resolving Enzyme -

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Basic information

Entry
Database: PDB / ID: 1ob8
TitleHolliday Junction Resolving Enzyme
ComponentsHOLLIDAY-JUNCTION RESOLVASE
KeywordsHYDROLASE / ENZYME / HOMOLOGOUS RECOMBINATION / HOLLIDAY JUNCTION RESOLVING ENZYME / NUCLEASE / ARCHAEA / THERMOPHILE
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / nucleic acid 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 Hje
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMiddleton, C.L. / Parker, J.L. / Richard, D.J. / White, M.F. / Bond, C.S.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Substrate Recognition and Catalysis by the Holliday Junction Resolving Enzyme Hje.
Authors: Middleton, C.L. / Parker, J.L. / Richard, D.J. / White, M.F. / Bond, C.S.
History
DepositionJan 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOLLIDAY-JUNCTION RESOLVASE
B: HOLLIDAY-JUNCTION RESOLVASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,71311
Polymers30,9502
Non-polymers7639
Water4,522251
1
A: HOLLIDAY-JUNCTION RESOLVASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9497
Polymers15,4751
Non-polymers4746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HOLLIDAY-JUNCTION RESOLVASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7634
Polymers15,4751
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.577, 90.577, 70.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 6 - 129 / Label seq-ID: 6 - 129

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.269421, -0.391712, -0.879758), (-0.352693, -0.809932, 0.468633), (-0.896114, 0.436544, 0.080059)
Vector: 55.6985, 80.7555, 12.5555)

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Components

#1: Protein HOLLIDAY-JUNCTION RESOLVASE / HOLLIDAY JUNCTION ENDONUCLEASE


Mass: 15475.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET19B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q97YX6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.74 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / pH: 9
Details: 0.2M LITHIUM SULFATE,0.1M TRIS PH 9 20% PEG 4000,15% ETHYLENE GLYCOL,293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.86
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 4, 2002 / Details: RH COATED SI MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 30127 / % possible obs: 98 % / Redundancy: 4.25 % / Rsym value: 0.033 / Net I/σ(I): 41.1
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 1.75 / Rsym value: 0.652 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SE-SAD DERIVED STRUCTURE

Resolution: 1.8→24.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.799 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1503 5 %RANDOM
Rwork0.197 ---
obs-28499 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 42 251 2282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222139
X-RAY DIFFRACTIONr_bond_other_d0.0020.022071
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9942882
X-RAY DIFFRACTIONr_angle_other_deg0.76734861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022178
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02382
X-RAY DIFFRACTIONr_nbd_refined0.1980.2432
X-RAY DIFFRACTIONr_nbd_other0.2330.22677
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1020.21425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8321.51244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53522064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7213895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9694.5817
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1832 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal0.882
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 97
Rwork0.274 2007

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