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- PDB-3k5o: Crystal structure of E.coli Pol II -

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Basic information

Entry
Database: PDB / ID: 3k5o
TitleCrystal structure of E.coli Pol II
ComponentsDNA polymerase II
KeywordsTRANSFERASE / Apo / DNA damage / DNA repair / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase / SOS response
Function / homology
Function and homology information


3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase B, N domain, beta-barrel / B family DNA polymerase, N domain, alpha/beta motif / Helix Hairpins - #1130 / : / DNA polymerase II, N-terminal / DNA polymerase II, insertion domain / B family DNA polymerase, thumb domain / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain ...DNA polymerase B, N domain, beta-barrel / B family DNA polymerase, N domain, alpha/beta motif / Helix Hairpins - #1130 / : / DNA polymerase II, N-terminal / DNA polymerase II, insertion domain / B family DNA polymerase, thumb domain / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : / DNA polymerase family B, thumb domain / 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 / Topoisomerase I; Chain A, domain 4 / Helix Hairpins / 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 / Helix non-globular / Ribonuclease H-like superfamily/Ribonuclease H / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, W. / Wang, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structural insight into translesion synthesis by DNA Pol II.
Authors: Wang, F. / Yang, W.
History
DepositionOct 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase II
B: DNA polymerase II


Theoretical massNumber of molelcules
Total (without water)180,9192
Polymers180,9192
Non-polymers00
Water9,404522
1
A: DNA polymerase II


Theoretical massNumber of molelcules
Total (without water)90,4601
Polymers90,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA polymerase II


Theoretical massNumber of molelcules
Total (without water)90,4601
Polymers90,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.849, 116.820, 163.461
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 II / Pol II


Mass: 90459.734 Da / Num. of mol.: 2 / Mutation: D335N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0060, dinA, JW0059, polB / Plasmid: Modified PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21189, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Na Citrate, 10% PEG4000, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 91060 / Num. obs: 89965 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8985 / % possible all: 99.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q8I

1q8i


Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2029 2.2 %RANDOM
Rwork0.218 80741 --
obs-82770 --
Solvent computationBsol: 39.734 Å2
Displacement parametersBiso max: 91.35 Å2 / Biso mean: 39.287 Å2 / Biso min: 12.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.773 Å20 Å20 Å2
2--1.635 Å20 Å2
3----4.409 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.28 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12152 0 0 522 12674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.724
X-RAY DIFFRACTIONc_mcbond_it1.3091.5
X-RAY DIFFRACTIONc_scbond_it1.9832
X-RAY DIFFRACTIONc_mcangle_it2.1712
X-RAY DIFFRACTIONc_scangle_it2.9812.5
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection
Rfree0.306 176
Rwork0.283 -
obs-7500

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