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- PDB-2oca: The crystal structure of T4 UvsW -

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Basic information

Entry
Database: PDB / ID: 2oca
TitleThe crystal structure of T4 UvsW
ComponentsATP-dependent DNA helicase uvsW
KeywordsHYDROLASE / ATP-dependant helicase / T4-bacteriophage / Recombination
Function / homology
Function and homology information


helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Translation Initiation Factor Eif1 - #20 / UvsW.1 domain / DNA helicase UvsW superfamily / : / : / UvsW.1 domain / DNA helicase UvsW, N-terminal / : / Translation Initiation Factor Eif1 / Helicase/UvrB, N-terminal ...Translation Initiation Factor Eif1 - #20 / UvsW.1 domain / DNA helicase UvsW superfamily / : / : / UvsW.1 domain / DNA helicase UvsW, N-terminal / : / Translation Initiation Factor Eif1 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase uvsW
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKerr, I.D. / White, S.W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystallographic and NMR Analyses of UvsW and UvsW.1 from Bacteriophage T4.
Authors: Kerr, I.D. / Sivakolundu, S. / Li, Z. / Buchsbaum, J.C. / Knox, L.A. / Kriwacki, R. / White, S.W.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999 SEQUENCE AUTHORS STATE THAT THE DIFFERENCE BETWEEN THEIR CLONED SEQUENCE AND THE DATABASE SEQUENCE ... SEQUENCE AUTHORS STATE THAT THE DIFFERENCE BETWEEN THEIR CLONED SEQUENCE AND THE DATABASE SEQUENCE AT POSITION 457 REPRESENTS VARIATION IN THE PHAGE SEQUENCE AND NOT A MUTATION INCORPORATED BY AMPLIFICATION OF THE GENE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase uvsW


Theoretical massNumber of molelcules
Total (without water)58,9561
Polymers58,9561
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.640, 155.200, 101.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ATP-dependent DNA helicase uvsW / Dar protein


Mass: 58955.855 Da / Num. of mol.: 1 / Mutation: K141R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: uvsW, dar / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus / References: UniProt: P20703, ATP diphosphatase
#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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 8, 2006
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 2003 / Num. obs: 25580 / % possible obs: 97.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.082 / Χ2: 2.285 / Net I/σ(I): 35.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.15 / Χ2: 1.629 / % possible all: 82.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.02 Å47.42 Å
Translation3.02 Å47.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RIF

1rif


Resolution: 2.7→30 Å / FOM work R set: 0.821 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Atoms at 0.00 occupancy have little or no electron density and were modelled stereochemically. Residues 287-295 are missing due to insufficient electron density
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1292 5 %Random
Rwork0.217 ---
obs-25425 97.5 %-
Solvent computationBsol: 50.771 Å2
Displacement parametersBiso mean: 69.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.783 Å20 Å20 Å2
2--30.546 Å20 Å2
3----15.762 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 0 106 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.261
X-RAY DIFFRACTIONc_mcbond_it1.3441.5
X-RAY DIFFRACTIONc_scbond_it2.0182
X-RAY DIFFRACTIONc_mcangle_it2.3312
X-RAY DIFFRACTIONc_scangle_it3.1262.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.740.393380.342756794
2.74-2.780.325570.319826883
2.78-2.820.362560.326862918
2.82-2.860.294510.308895946
2.86-2.910.291440.281914958
2.91-2.960.315500.2679771027
2.96-3.010.299400.2669691009
3.01-3.070.304600.2579911051
3.07-3.130.248540.2499831037
3.13-3.20.373560.2529751031
3.2-3.280.321620.2339741036
3.28-3.360.254630.2339571020
3.36-3.450.224590.2079751034
3.45-3.550.228680.1979701038
3.55-3.660.216410.1849861027
3.66-3.790.202530.18510021055
3.79-3.950.23560.1889811037
3.95-4.120.275440.1939991043
4.12-4.340.201620.1849761038
4.34-4.610.21580.16910001058
4.61-4.970.194430.17910061049
4.97-5.460.259460.19910141060
5.46-6.250.361490.26610201069
6.25-7.850.24410.24610401081
7.85-300.221410.22510851126
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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