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- PDB-3k57: Crystal structure of E.coli Pol II-normal DNA-dATP ternary complex -

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Basic information

Entry
Database: PDB / ID: 3k57
TitleCrystal structure of E.coli Pol II-normal DNA-dATP ternary complex
Components
  • DNA (5'-D(*G*TP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*G)-3')
  • DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*(DOC))-3')
  • DNA polymerase II
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DNA damage / DNA repair / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase / SOS response / Transferase / TRANSFERASE-DNA COMPLEX
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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 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 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase II
T: DNA (5'-D(*G*TP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*G)-3')
P: DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5086
Polymers99,9683
Non-polymers5403
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-41 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.425, 99.888, 125.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase II / Pol II


Mass: 90459.734 Da / Num. of mol.: 1 / 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 with prescission protease cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21189, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*G*TP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*G)-3')


Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis
#3: DNA chain DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*(DOC))-3')


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis

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Non-polymers , 3 types, 528 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 20% PEGmme5000, 0.2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Oct 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→20 Å / Num. all: 61590 / Num. obs: 57617 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6065 / % possible all: 87

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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: 2.08→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 1351 Random
Rwork0.204 --
all-61438 -
obs-53505 -
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6343 609 32 525 7509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.487
X-RAY DIFFRACTIONc_dihedral_angle_d23.29
X-RAY DIFFRACTIONc_improper_angle_d1.315
LS refinement shellResolution: 2.08→2.15 Å
RfactorNum. reflection
Rfree0.281 4370
Rwork0.293 -
obs-4480

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