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- PDB-1ih7: High-Resolution Structure of Apo RB69 DNA Polymerase -

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Basic information

Entry
Database: PDB / ID: 1ih7
TitleHigh-Resolution Structure of Apo RB69 DNA Polymerase
ComponentsDNA POLYMERASE
KeywordsTRANSFERASE / DNA polymerase / fingers / palm / thumb
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
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 polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / 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 / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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 / SYNCHROTRON / phase extension / Resolution: 2.21 Å
AuthorsFranklin, M.C. / Wang, J. / Steitz, T.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of the Replicating Complex of a Pol alpha Family DNA Polymerase
Authors: Franklin, M.C. / Wang, J. / Steitz, T.A.
#1: 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.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Building a Replisome from Interacting Pieces: Sliding Clamp Complexed to a Peptide from DNA Polymerase and a Polymerase Editing Complex
Authors: Shamoo, Y. / Steitz, T.A.
History
DepositionApr 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1054
Polymers104,7431
Non-polymers3613
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.196, 116.309, 194.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach monomer constitutes a functional assembly.

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Components

#1: Protein DNA POLYMERASE / GP43


Mass: 104743.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: gp43 / Plasmid: pRB.43 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium citrate, sodium/potassium tartrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6.25 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlpolymerase1drop
21 mMdTTP1drop
3200 mM1reservoirCaCl2
430 %(w/v)PEG350 MME1reservoir
5100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.913 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 1999 / Details: double crystal monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 88785 / Num. obs: 88785 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3 / Num. unique all: 4352 / % possible all: 98.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: phase extension
Starting model: PDB entry 1WAJ, with all non-protein atoms removed

1waj


Resolution: 2.21→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 533579.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh and Huber, as implemented in CNS
Details: This refinement extended the previous apo-RB69 polymerase structure to higher resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 6671 7.9 %RANDOM
Rwork0.215 ---
all0.215 84918 --
obs0.215 84918 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.24 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 48.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---7.2 Å20 Å2
3---5.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.21→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7339 0 22 342 7703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.088
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it1.352
X-RAY DIFFRACTIONc_mcangle_it2.163
X-RAY DIFFRACTIONc_scbond_it3.894
X-RAY DIFFRACTIONc_scangle_it5.65
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 181 10.6 %
Rwork0.328 1519 -
obs-1491 36.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GNS.PARGNS.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor all: 10
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it4
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it5
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.328

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