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- PDB-3rmd: Crystal Structure of a replicative DNA polymerase bound to DNA co... -

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Basic information

Entry
Database: PDB / ID: 3rmd
TitleCrystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
Components
  • DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA LESION / THYMINE GLYCOL / PROTEIN-DNA COMPLEX / TRANSFERASE-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / 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 / : ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / 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 / : / Monooxygenase / 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 / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.98 Å
AuthorsAller, P. / Duclos, S. / Wallace, S.S. / Doublie, S.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.
Authors: Aller, P. / Duclos, S. / Wallace, S.S. / Doublie, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.
Authors: Aller, P. / Rould, M.A. / Hogg, M. / Wallace, S.S. / Doublie, S.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
B: DNA polymerase
C: DNA polymerase
D: DNA polymerase
E: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
F: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
G: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
H: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
I: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
J: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
K: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
L: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,90314
Polymers460,92112
Non-polymers9822
Water3,387188
1
A: DNA polymerase
E: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
F: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)115,2303
Polymers115,2303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-25 kcal/mol
Surface area44660 Å2
MethodPISA
2
B: DNA polymerase
G: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
H: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7214
Polymers115,2303
Non-polymers4911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-25 kcal/mol
Surface area43870 Å2
MethodPISA
3
C: DNA polymerase
I: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
J: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7214
Polymers115,2303
Non-polymers4911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-30 kcal/mol
Surface area44030 Å2
MethodPISA
4
D: DNA polymerase
K: DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
L: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)115,2303
Polymers115,2303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-25 kcal/mol
Surface area43550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.837, 123.025, 168.775
Angle α, β, γ (deg.)90.000, 95.870, 90.000
Int Tables number4
Space group name H-MP1211
Details4 complexes DNA/DNA-polymerase per asymmetric unit

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Components

#1: Protein
DNA polymerase / Gp43


Mass: 105069.586 Da / Num. of mol.: 4 / Mutation: D222A, D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')


Mass: 5575.606 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA template
#3: DNA chain
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3')


Mass: 4584.985 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA primer
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 4% PEG 20,000, 100 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2007 / Details: Rhodium coated silicon single crysta
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. all: 111177 / Num. obs: 109082 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.092 / Χ2: 1.063 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.98-3.093.10.40991360.953182.5
3.09-3.214.10.372109120.971199.1
3.21-3.364.70.284110630.969199.9
3.36-3.534.80.206110711.0811100
3.53-3.754.80.153110861.1171100
3.75-4.044.80.109111091.1181100
4.04-4.454.90.077111191.0561100
4.45-5.094.90.063110941.0531100
5.09-6.424.80.062111681.0841100
6.42-504.70.046113241.142199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: pdb entry 2DY4

2dy4


Resolution: 2.98→50 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 19418 8.9 %RANDOM
Rwork0.22 ---
obs-106834 92.8 %-
Solvent computationBsol: 49.9206 Å2
Displacement parametersBiso max: 200.13 Å2 / Biso mean: 67.1825 Å2 / Biso min: 2.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.326 Å20 Å29.771 Å2
2---2.51 Å20 Å2
3---1.184 Å2
Refinement stepCycle: LAST / Resolution: 2.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29076 2546 60 188 31870
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.277
X-RAY DIFFRACTIONc_mcbond_it1.2881.5
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_mcangle_it2.2832
X-RAY DIFFRACTIONc_scangle_it2.9462.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna-test.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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