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- PDB-3k5m: Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ter... -

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Basic information

Entry
Database: PDB / ID: 3k5m
TitleCrystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ternary complex
Components
  • DNA (5'-D(*AP*GP*TP*CP*CP*TP*GP*(3DR)P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')
  • DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3')
  • DNA polymerase II
KeywordsTRANSFERASE/DNA / 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'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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: 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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _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(*AP*GP*TP*CP*CP*TP*GP*(3DR)P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')
P: DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0346
Polymers100,4623
Non-polymers5713
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-43 kcal/mol
Surface area37160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.109, 95.228, 144.735
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 / 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(*AP*GP*TP*CP*CP*TP*GP*(3DR)P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')


Mass: 5994.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Abasic Lt(-2, 2) template
#3: DNA chain DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3')


Mass: 4007.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer

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Non-polymers , 3 types, 494 molecules

#4: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-25% PEGMME3350, 0.1 M ammonium formate, 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: Jan 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 65181 / Num. obs: 62414 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6409 / % possible all: 98.7

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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 3K59

3k59


Resolution: 2.04→28.43 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1450 2.2 %Random
Rwork0.243 56213 --
obs-57663 88.7 %-
Solvent computationBsol: 51.775 Å2
Displacement parametersBiso max: 82.82 Å2 / Biso mean: 34.132 Å2 / Biso min: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-5.759 Å20 Å20 Å2
2---2.918 Å20 Å2
3----2.841 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.04→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 663 32 491 7390
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d1.707
X-RAY DIFFRACTIONc_mcbond_it1.2121.5
X-RAY DIFFRACTIONc_scbond_it1.7922
X-RAY DIFFRACTIONc_mcangle_it1.8252
X-RAY DIFFRACTIONc_scangle_it2.5362.5
LS refinement shellResolution: 2.04→2.11 Å
RfactorNum. reflection
Rfree0.319 132
Rwork0.309 -
obs-5369
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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