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

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Basic information

Entry
Database: PDB / ID: 3maq
TitleCrystal structure of E.coli Pol II-normal DNA-dGTP ternary complex
Components
  • DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*(DOC))-3')
  • DNA (5'-D(*TP*AP*CP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-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


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / 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 / B family DNA polymerase, thumb domain / Topoisomerase I; Chain A, domain 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb 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 / B family DNA polymerase, thumb domain / Topoisomerase I; Chain A, domain 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm 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 / Helix Hairpins / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 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
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionApr 7, 2010ID: 3K5A
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 6, 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_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_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(*TP*AP*CP*GP*TP*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*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1636
Polymers99,6083
Non-polymers5563
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-37 kcal/mol
Surface area37770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.931, 100.727, 126.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailstrimer

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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(*TP*AP*CP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')


Mass: 5196.387 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, 394 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#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.: 391 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
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: Feb 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 40951 / Num. obs: 40765 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4025 / % possible all: 99.7

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Processing

Software
NameClassification
StructureStudiodata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3K57

3k57


Resolution: 2.4→30 Å / Cross valid method: Thoughout / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.223 932 RANDOM
Rwork0.216 --
obs0.237 37503 -
all-41034 -
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 607 33 391 7337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d1.811
X-RAY DIFFRACTIONc_dihedral_angle_d25.054
X-RAY DIFFRACTIONc_improper_angle_d1.976
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection
Rfree0.271 88
Rwork0.267 -
obs-3387

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