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- PDB-1cr4: CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF... -

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Entry
Database: PDB / ID: 1cr4
TitleCRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DTDP
ComponentsDNA PRIMASE/HELICASE
KeywordsTRANSFERASE / RECA-TYPE PROTEIN FOLD
Function / homology
Function and homology information


DNA primase activity / viral DNA genome replication / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / single-stranded DNA binding / 5'-3' DNA helicase activity / 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
THYMIDINE-5'-DIPHOSPHATE / DNA helicase/primase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSawaya, M.R. / Guo, S. / Tabor, S. / Richardson, C.C. / Ellenberger, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7.
Authors: Sawaya, M.R. / Guo, S. / Tabor, S. / Richardson, C.C. / Ellenberger, T.
History
DepositionAug 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _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 7, 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 PRIMASE/HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4264
Polymers32,8321
Non-polymers5943
Water27015
1
A: DNA PRIMASE/HELICASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)200,55824
Polymers196,9926
Non-polymers3,56618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
crystal symmetry operation3_555-x+y,-x,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+5/61
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)80.784, 80.784, 85.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe filament may be generated by applying the crystallographic 6 sub 1 screw operator

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Components

#1: Protein DNA PRIMASE/HELICASE


Mass: 32831.977 Da / Num. of mol.: 1 / Fragment: HELICASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Plasmid: PET17B / Production host: Escherichia coli (E. coli)
References: UniProt: P03692, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: AMMONIUM SULFATE, ACES, pH 9.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-35 mg/mlprotein1drop
210 mMlithium sulfate1drop
320 mMTris-HCl1drop
45 mMdithiothreitol1drop
51.4-1.6 Mammonium sulfate1reservoir
6100 mMACES1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 10706 / Num. obs: 10706 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 30
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 7 % / Rmerge(I) obs: 0.453 / % possible all: 100
Reflection
*PLUS
Num. measured all: 27233
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1070 10 %RANDOM
Rwork0.242 ---
all0.251 0 --
obs0.251 10706 100 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 35 15 1890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.016

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