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- PDB-3a2f: Crystal Structure of Pyrococcus furiosus DNA polymerase/PCNA mono... -

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Basic information

Entry
Database: PDB / ID: 3a2f
TitleCrystal Structure of Pyrococcus furiosus DNA polymerase/PCNA monomer mutant complex
Components
  • DNA polymerase sliding clampDNA clamp
  • DNA polymerase
KeywordsTRANSFERASE/REPLICATION / DNA replication / DNA-binding / DNA-directed DNA polymerase / Endonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / TRANSFERASE-REPLICATION COMPLEX
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / endonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / DNA polymerase family B, thumb 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-directed DNA polymerase, family B, multifunctional 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp / DNA polymerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.67 Å
AuthorsNishida, H. / Ishino, Y. / Morikawa, K.
CitationJournal: To be Published
Title: Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex
Authors: Nishida, H. / Mayanagi, K. / Kiyonari, S. / Sato, Y. / Ishino, Y. / Morikawa, K.
History
DepositionMay 15, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 sliding clamp


Theoretical massNumber of molelcules
Total (without water)118,8972
Polymers118,8972
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area46700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.354, 90.451, 186.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase / / replicative B-type polymerase / Pfu polymerase


Mass: 90723.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: pol, PF0212 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61875, DNA-directed DNA polymerase
#2: Protein DNA polymerase sliding clamp / DNA clamp / DNA clamp / Proliferating cell nuclear antigen homolog / PCNA


Mass: 28174.158 Da / Num. of mol.: 1 / Mutation: M73L, D143A, D147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: pcn, PF0983 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O73947
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 30%(w/v) PEG 5000, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.0, 0.9641, 0.9791, 0.9794, 0.9951
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2007
RadiationMonochromator: mirros / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.96411
30.97911
40.97941
50.99511
ReflectionResolution: 2.67→50 Å / Num. all: 39950 / Num. obs: 37495 / % possible obs: 98.8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.7
Reflection shellResolution: 2.67→2.77 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 4.2 / % possible all: 89.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.67→46.55 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.883 / Rfactor Rfree error: 0.007 / SU B: 33.287 / SU ML: 0.344 / Data cutoff high absF: 2842515.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.164 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1867 5 %RANDOM
Rwork0.241 ---
obs0.241 37422 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.3024 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2--1.75 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.67→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8128 0 0 126 8254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.67→2.84 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 291 5.1 %
Rwork0.336 5463 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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