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- PDB-1waf: DNA POLYMERASE FROM BACTERIOPHAGE RB69 -

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Basic information

Entry
Database: PDB / ID: 1waf
TitleDNA POLYMERASE FROM BACTERIOPHAGE RB69
ComponentsDNA POLYMERASE
KeywordsNUCLEOTIDYLTRANSFERASE / RB69 DNA POLYMERASE (GP43)
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : / Monooxygenase / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.2 Å
AuthorsWang, J. / Satter, A.K.M.A. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.
Authors: Wang, J. / Sattar, A.K. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A.
#1: Journal: To be Published
Title: Structural Basis for Phenotypes of Mutant Pol Alpha Family DNA Polymerases
Authors: Wang, J. / Steitz, T.
#2: Journal: Biochemistry / Year: 1996
Title: Crystal Structures of an NH2-Terminal Fragment of T4 DNA Polymerase and its Complexes with Single-Stranded DNA and with Divalent Metal Ions
Authors: Wang, J. / Yu, P. / Lin, T.C. / Konigsberg, W.H. / Steitz, T.A.
#3: Journal: J.Biol.Chem. / Year: 1995
Title: Modular Organization of T4 DNA Polymerase. Evidence from Phylogenetics
Authors: Wang, C.C. / Yeh, L.S. / Karam, J.D.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Primary Structure of T4 DNA Polymerase. Evolutionary Relatedness to Eucaryotic and Other Procaryotic DNA Polymerases
Authors: Spicer, E.K. / Rush, J. / Fung, C. / Reha-Krantz, L.J. / Karam, J.D. / Konigsberg, W.H.
History
DepositionApr 13, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE
B: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,0534
Polymers209,4862
Non-polymers5662
Water00
1
A: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0262
Polymers104,7431
Non-polymers2831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0262
Polymers104,7431
Non-polymers2831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.320, 196.860, 118.310
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA POLYMERASE / T4 GP43


Mass: 104743.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: POL / Gene (production host): POL / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5

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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: 4.9 Å3/Da / Density % sol: 80 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Density % sol: 75 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
20.05 Msodium citrate1reservoir
30.025 Msodium potassium tartrate1reservoir
40.25 M1reservoirLi2SO4
50.25 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Sep 1, 1994 / Details: MIRROR
RadiationMonochromator: MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 60256 / % possible obs: 91 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.145

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 3.2→40 Å / σ(F): 2
RfactorNum. reflection
Rfree0.274 -
Rwork0.198 -
obs0.198 47783
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14758 0 80 0 14838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.2
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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