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- PDB-2zj2: Archaeal DNA helicase Hjm apo state in form 1 -

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Basic information

Entry
Database: PDB / ID: 2zj2
TitleArchaeal DNA helicase Hjm apo state in form 1
ComponentsPutative ski2-type helicase
KeywordsHYDROLASE / RecA fold / ATP-binding / Helicase / Nucleotide-binding
Function / homology
Function and homology information


DNA 3'-5' helicase / 3'-5' DNA helicase activity / isomerase activity / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Sec63 N-terminal domain-like fold - #20 / ATP-dependent DNA helicase Hel308 / : / Archaeal helicase, domain 4 / Sec63 N-terminal domain-like fold / Helix-hairpin-helix motif / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / DEAD/DEAH box helicase ...Sec63 N-terminal domain-like fold - #20 / ATP-dependent DNA helicase Hel308 / : / Archaeal helicase, domain 4 / Sec63 N-terminal domain-like fold / Helix-hairpin-helix motif / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase Hel308
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsOyama, T. / Oka, H. / Fujikane, R. / Ishino, Y. / Morikawa, K.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm
Authors: Oyama, T. / Oka, H. / Mayanagi, K. / Shirai, T. / Matoba, K. / Fujikane, R. / Ishino, Y. / Morikawa, K.
History
DepositionFeb 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ski2-type helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2276
Polymers82,7461
Non-polymers4805
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative ski2-type helicase
hetero molecules

A: Putative ski2-type helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,45312
Polymers165,4932
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5990 Å2
ΔGint-167.5 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.269, 83.441, 95.019
Angle α, β, γ (deg.)90.00, 120.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-901-

SO4

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Components

#1: Protein Putative ski2-type helicase / DNA helicase


Mass: 82746.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: peT21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O73946, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6M Ammonium suflate, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2004 / Details: SI
RadiationMonochromator: K-B MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 31018 / Num. obs: 30454 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.375 / Num. unique all: 2838 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→44.86 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 348188.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1481 5 %RANDOM
Rwork0.228 ---
obs0.228 29821 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6782 Å2 / ksol: 0.371661 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.66 Å20 Å21.84 Å2
2---1.12 Å20 Å2
3---5.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 25 90 5316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it16.531.5
X-RAY DIFFRACTIONc_mcangle_it15.862
X-RAY DIFFRACTIONc_scbond_it19.242
X-RAY DIFFRACTIONc_scangle_it17.992.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 217 4.7 %
Rwork0.335 4353 -
obs--88.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4so4.paramso4.top

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