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- PDB-1x2i: Crystal Structure Of Archaeal Xpf/Mus81 Homolog, Hef From Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 1x2i
TitleCrystal Structure Of Archaeal Xpf/Mus81 Homolog, Hef From Pyrococcus Furiosus, Helix-hairpin-helix Domain
ComponentsHef helicase/nuclease
KeywordsHYDROLASE / alpha helix / helix-hairpin-helix DNA binding domain / homodimer
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
Archaeal Hef helicase/nuclease, insert domain / Putative ATP-dependent RNA helicase, helical bundle / 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 ...Archaeal Hef helicase/nuclease, insert domain / Putative ATP-dependent RNA helicase, helical bundle / 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 / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / 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 nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent RNA helicase, putative
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsNishino, T. / Komori, K. / Ishino, Y. / Morikawa, K.
CitationJournal: STRUCTURE / Year: 2005
Title: Structural and Functional Analyses of an Archaeal XPF/Rad1/Mus81 Nuclease: Asymmetric DNA Binding and Cleavage Mechanisms
Authors: Nishino, T. / Komori, K. / Ishino, Y. / Morikawa, K.
History
DepositionApr 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hef helicase/nuclease
B: Hef helicase/nuclease


Theoretical massNumber of molelcules
Total (without water)16,9762
Polymers16,9762
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-14 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.942, 56.889, 68.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 8487.955 Da / Num. of mol.: 2 / Fragment: Helix-hairpin-helix DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF2015 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8TZH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.16 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: trypsin, Na-Malonate, pH 7.0, EVAPORATION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL38B120.9729, 0.97774, 0.97779, 0.9757
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDOct 21, 2002
MARRESEARCH2CCDOct 21, 2002graphite
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE-CRYSTALSINGLE WAVELENGTHMx-ray1
2DiamondMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97291
30.977741
40.977791
50.97571
ReflectionResolution: 1.45→20 Å / Num. obs: 27454 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.061
Reflection shellResolution: 1.45→1.5 Å / Rsym value: 0.104 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.45→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2383 2717 random
Rwork0.2218 --
all0.2234 28301 -
obs0.2234 27184 -
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 0 125 1191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d0.7099
X-RAY DIFFRACTIONc_dihedral_angle_d18.37
X-RAY DIFFRACTIONc_bond_d0.003692
X-RAY DIFFRACTIONc_angle_d1.02152
LS refinement shellResolution: 1.45→1.5 Å
RfactorNum. reflection% reflection
Rfree0.2472 252 -
Rwork0.2103 --
obs-2685 96.72 %

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