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- PDB-1rif: Crystal structure of the UvsW helicase from Bacteriophage T4 -

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Basic information

Entry
Database: PDB / ID: 1rif
TitleCrystal structure of the UvsW helicase from Bacteriophage T4
ComponentsDNA helicase uvsW
KeywordsDNA BINDING PROTEIN / Bacteriophage / T4 / Helicase / UvsW / RecG / SF2
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 / Type III restriction enzyme, res subunit ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / MAD / Resolution: 2 Å
AuthorsSickmier, E.A. / White, S.W. / Kreuzer, K.N.
CitationJournal: Structure / Year: 2004
Title: The Crystal Structure of the UvsW Helicase from Bacteriophage T4.
Authors: Sickmier, E.A. / Kreuzer, K.N. / White, S.W.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA helicase uvsW
B: DNA helicase uvsW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5529
Polymers65,6912
Non-polymers8617
Water4,576254
1
A: DNA helicase uvsW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2644
Polymers32,8461
Non-polymers4183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA helicase uvsW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2885
Polymers32,8461
Non-polymers4434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.739, 95.181, 86.278
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA helicase uvsW / Dar protein


Mass: 32845.562 Da / Num. of mol.: 2 / 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P20703
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Amonium sulfate, magnesium chloride, Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
225 %PEG33501reservoir
3100 mMTris-HCl1reservoirpH7.5
4200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0383, 1.03900
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03831
21.0391
ReflectionResolution: 2→20 Å / Num. all: 46444 / Num. obs: 42780 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Rsym value: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.03 Å / Num. unique all: 1722 / % possible all: 74.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 2042 Random
Rwork0.218 --
all0.221 40844 -
obs0.221 40844 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 7 254 4891
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. reflection obs: 36756 / Num. reflection Rfree: 4128
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.007
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.34
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg23.45
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.7

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