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- PDB-1noz: T4 DNA POLYMERASE FRAGMENT (RESIDUES 1-388) AT 110K -

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Basic information

Entry
Database: PDB / ID: 1noz
TitleT4 DNA POLYMERASE FRAGMENT (RESIDUES 1-388) AT 110K
ComponentsDNA POLYMERASE
KeywordsNUCLEOTIDYLTRANSFERASE / EXONUCLEASE / DNA-BINDING
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-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain ...DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / 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 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWang, J. / Yu, P. / Lin, T.C. / Konigsberg, W.H. / Steitz, T.A.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Isolation, Characterization, and Kinetic Properties of Truncated Forms of T4 DNA Polymerase that Exhibit 3'-5' Exonuclease Activity
Authors: Lin, T.C. / Karam, G. / Konigsberg, W.H.
#2: 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
DepositionFeb 16, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE
B: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)90,6312
Polymers90,6312
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-22 kcal/mol
Surface area30840 Å2
MethodPISA
2
A: DNA POLYMERASE
B: DNA POLYMERASE

A: DNA POLYMERASE
B: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)181,2634
Polymers181,2634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7980 Å2
ΔGint-59 kcal/mol
Surface area59320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.617, 109.309, 68.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA POLYMERASE / T4 GP43 N388


Mass: 45315.727 Da / Num. of mol.: 2 / Fragment: RESIDUES 1 - 388
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P04415, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Msodium formate11
25 mMTris-HCl11
30.1 mMEDTA12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 7, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection% possible obs: 100 %
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.096

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Processing

Software
NameClassification
DCREDUCEdata collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
DCREDUCEdata reduction
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2
Details: THIS STRUCTURE WAS DETERMINED AT LN2 TEMPERATURE (110K). THE DIVALENT AND P(DT)3 WERE DETERMINED FROM TWO SEPARATE EXPERIMENTS AT LOWER RESOLUTIONS, CONCATENATED TOGETHER IN THIS ENTRY. ASP ...Details: THIS STRUCTURE WAS DETERMINED AT LN2 TEMPERATURE (110K). THE DIVALENT AND P(DT)3 WERE DETERMINED FROM TWO SEPARATE EXPERIMENTS AT LOWER RESOLUTIONS, CONCATENATED TOGETHER IN THIS ENTRY. ASP 1, GLU 2, ILE 211 AND FOUR OTHER RESIDUES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS, BUT THE AUTHORS HAVE NOT DONE DNA SEQUENCING TO CONFIRM POSSIBLE SPONTANEOUSLY MUTATIONS. ILE 211 WAS REPLACED BY THR 211 IN THIS ENTRY WITHOUT ADDITIONAL REFINEMENT BY REMOVING ATOM CD1.
RfactorNum. reflection
Rwork0.222 -
obs0.222 37292
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 0 45 5941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.54
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
Biso mean: 41 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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