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- PDB-1e0j: gp4d helicase from phage T7 ADPNP complex -

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Basic information

Entry
Database: PDB / ID: 1e0j
Titlegp4d helicase from phage T7 ADPNP complex
ComponentsDNA HELICASEHelicase
KeywordsHELICASE / ATPASE / DNA REPLICATION
Function / homology
Function and homology information


DNA primase activity / 5'-3' DNA helicase activity / viral DNA genome replication / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / single-stranded DNA binding / DNA helicase / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Bacteriophage T7 DNA helicase/primase / : / Bacteriophage T7 DNA helicase/primase, N-terminal a+b fold / Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal / Zinc-binding domain of primase-helicase / Zinc-binding domain of primase-helicase / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / Toprim-like / DnaB-like helicase C terminal domain ...Bacteriophage T7 DNA helicase/primase / : / Bacteriophage T7 DNA helicase/primase, N-terminal a+b fold / Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal / Zinc-binding domain of primase-helicase / Zinc-binding domain of primase-helicase / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / Toprim-like / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / TOPRIM / Toprim domain profile. / TOPRIM domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA helicase/primase
Similarity search - Component
Biological speciesPHAGE T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSingleton, M.R. / Sawaya, M.R. / Ellenberger, T. / Wigley, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides
Authors: Singleton, M.R. / Sawaya, M.R. / Ellenberger, T. / Wigley, D.B.
History
DepositionMar 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA HELICASE
B: DNA HELICASE
C: DNA HELICASE
D: DNA HELICASE
E: DNA HELICASE
F: DNA HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,65314
Polymers190,5316
Non-polymers2,1228
Water0
1
A: DNA HELICASE
B: DNA HELICASE
C: DNA HELICASE
hetero molecules

A: DNA HELICASE
B: DNA HELICASE
C: DNA HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,65314
Polymers190,5316
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
2
D: DNA HELICASE
E: DNA HELICASE
F: DNA HELICASE
hetero molecules

D: DNA HELICASE
E: DNA HELICASE
F: DNA HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,65314
Polymers190,5316
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)119.180, 119.180, 283.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
DNA HELICASE / Helicase


Mass: 31755.139 Da / Num. of mol.: 6 / Fragment: DOMAIN 4D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHAGE T7 (virus) / Gene: GENE 4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03692
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growpH: 9.5 / Details: pH 9.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 40673 / % possible obs: 97.9 % / Redundancy: 3 % / Rsym value: 0.065 / Net I/σ(I): 16.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rsym value: 0.304 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.304 2107 5.2 %RANDOM
Rwork0.253 ---
obs0.253 40644 96.7 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13264 0 128 0 13392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 379 5.8 %
Rwork0.37 6196 -
obs--96.7 %

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