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- PDB-4tkd: Sulfolobus solfataricus HJC mutants -

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Basic information

Entry
Database: PDB / ID: 4tkd
TitleSulfolobus solfataricus HJC mutants
ComponentsHolliday junction resolvase Hjc
KeywordsHYDROLASE
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
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBond, C.S.
CitationJournal: Aust.J.Chem. / Year: 2014
Title: Crystal Unengineering: Reducing the Crystallisability of Sulfolobus solfataricus Hjc
Authors: Middleton, C.L. / Parker, J.L. / Knott, G.J. / White, M.F. / Bond, C.S.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Holliday junction resolvase Hjc
B: Holliday junction resolvase Hjc
C: Holliday junction resolvase Hjc
D: Holliday junction resolvase Hjc


Theoretical massNumber of molelcules
Total (without water)63,1904
Polymers63,1904
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.601, 61.834, 55.245
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Holliday junction resolvase Hjc / Hjc


Mass: 15797.519 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: hjc, SSO0575, ORF-c21_024 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7LXU0, crossover junction endodeoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 10 % (w/v) PEG 6000, 5 % (v/v) PEG 400, and 0.1 M citric acid pH 5.0

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Data collection

DiffractionMean temperature: 103.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 21989 / % possible obs: 76.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.15 Å2 / Net I/σ(I): 15.2

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→19.93 Å / Cor.coef. Fo:Fc: 0.9374 / Cor.coef. Fo:Fc free: 0.9096 / SU R Cruickshank DPI: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.31 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1110 5.05 %RANDOM
Rwork0.1941 ---
obs0.1967 21985 75.86 %-
Displacement parametersBiso mean: 45.56 Å2
Baniso -1Baniso -2Baniso -3
1-7.4988 Å20 Å21.9244 Å2
2---4.677 Å20 Å2
3----2.8218 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: 1 / Resolution: 2.01→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 0 96 3859
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185080HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1444SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes545HARMONIC5
X-RAY DIFFRACTIONt_it3802HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion19.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion492SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4478SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.11 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2171 47 6.22 %
Rwork0.2333 709 -
all0.2322 756 -
obs--75.86 %

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