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- PDB-1j23: Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 1j23
TitleCrystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain
ComponentsATP-dependent RNA helicase, putative
KeywordsHYDROLASE / structure-specific endonuclease
Function / homology
Function and homology information


catalytic activity, acting on DNA / nuclease activity / helicase activity / DNA repair / DNA binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Archaeal Hef helicase/nuclease, insert domain / Putative ATP-dependent RNA helicase, helical bundle / Rossmann fold - #10130 / ERCC4 domain / ERCC4 domain / ERCC4 domain / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like ...Archaeal Hef helicase/nuclease, insert domain / Putative ATP-dependent RNA helicase, helical bundle / Rossmann fold - #10130 / ERCC4 domain / ERCC4 domain / ERCC4 domain / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase, putative
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsNishino, T. / Komori, K. / Ishino, Y. / Morikawa, K.
CitationJournal: Structure / Year: 2003
Title: X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
Authors: Nishino, T. / Komori, K. / Ishino, Y. / Morikawa, K.
History
DepositionDec 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase, putative


Theoretical massNumber of molelcules
Total (without water)16,1171
Polymers16,1171
Non-polymers00
Water1,910106
1
A: ATP-dependent RNA helicase, putative

A: ATP-dependent RNA helicase, putative


Theoretical massNumber of molelcules
Total (without water)32,2332
Polymers32,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Unit cell
Length a, b, c (Å)69.795, 69.795, 58.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by the two fold axis:x-y+1,2-y,-z-1/3

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Components

#1: Protein ATP-dependent RNA helicase, putative / Hef nuclease


Mass: 16116.660 Da / Num. of mol.: 1 / Fragment: nuclease domain fragment / Mutation: F55L, R63G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 codon plus RIL / References: UniProt: Q8TZH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.59 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 8
Details: Tricine-NaOH, NaCl, NaN3, subtilisin , pH 8.0, MICRODIALYSIS, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
160 mg/mlprotein11
2100 mMtricine-NaOH12pH8.0
3300 mM12NaCl
40.025 %12NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2001 / Details: diamond-graphite
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 16172 / Num. obs: 15983 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.7
Reflection shellResolution: 1.79→1.86 Å / Rmerge(I) obs: 0.173 / % possible all: 94.1
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
SOLVEphasing
CNS0.9refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD
Starting model: Selenomet-phased model

Resolution: 1.78→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 1589 random
Rwork0.219 --
all-15821 -
obs-14232 -
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 106 1135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.048
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.714
LS refinement shellResolution: 1.78→1.8 Å /
RfactorNum. reflection
Rfree0.244 34
Rwork0.257 -
obs-358
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.05
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.714

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