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- PDB-1wp9: Crystal structure of Pyrococcus furiosus Hef helicase domain -

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Basic information

Entry
Database: PDB / ID: 1wp9
TitleCrystal structure of Pyrococcus furiosus Hef helicase domain
ComponentsATP-dependent RNA helicase, putative
KeywordsHYDROLASE / Helicase / ATPase / DNA replication / DNA repair / DNA recombination
Function / homology
Function and homology information


catalytic activity, acting on DNA / DNA conformation change / nuclease activity / helicase activity / DNA repair / DNA binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
hef helicase domain / Archaeal Hef helicase/nuclease, insert domain / Putative ATP-dependent RNA helicase, helical bundle / phosphoenolpyruvate carboxylase, domain 3 / ERCC4 domain / ERCC4 domain / ERCC4 domain / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like ...hef helicase domain / Archaeal Hef helicase/nuclease, insert domain / Putative ATP-dependent RNA helicase, helical bundle / phosphoenolpyruvate carboxylase, domain 3 / 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 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ATP-dependent RNA helicase, putative
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsNishino, T. / Komori, K. / Tsuchiya, D. / Ishino, Y. / Morikawa, K.
CitationJournal: Structure / Year: 2005
Title: Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing
Authors: Nishino, T. / Komori, K. / Tsuchiya, D. / Ishino, Y. / Morikawa, K.
History
DepositionAug 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2019Group: Data collection / Refinement description / Category: refine_ls_shell / reflns / struct_biol
Item: _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase, putative
B: ATP-dependent RNA helicase, putative
C: ATP-dependent RNA helicase, putative
D: ATP-dependent RNA helicase, putative
E: ATP-dependent RNA helicase, putative
F: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,59612
Polymers338,0266
Non-polymers5706
Water88349
1
A: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,3381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,3381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,3381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,3381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,3381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ATP-dependent RNA helicase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,3381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.498, 165.940, 119.157
Angle α, β, γ (deg.)90.00, 114.85, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological assembly is assumed to be monomeric

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Components

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


Mass: 56337.691 Da / Num. of mol.: 6 / Fragment: residues 2-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: L2V / References: UniProt: Q8TZH8, EC: 3.6.1.3
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.14 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG 6000, 100mM Tricine-Na, 150mM NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.25 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2003
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 93081 / Num. obs: 92430 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.482 / % possible all: 93.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 9022 -random
Rwork0.257 ---
all0.286 89513 --
obs0.257 80491 97.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.5 Å
Luzzati sigma a0.69 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22834 0 30 49 22913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.38858
X-RAY DIFFRACTIONc_bond_d0.00877
X-RAY DIFFRACTIONc_dihedral_angle_d22.099
X-RAY DIFFRACTIONc_improper_angle_d0.84775
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.441 810 -
Rwork0.421 --
obs-7622 91.8 %

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