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- PDB-2dy4: Crystal structure of RB69 GP43 in complex with DNA containing Thy... -

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Basic information

Entry
Database: PDB / ID: 2dy4
TitleCrystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol
Components
  • 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
  • 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA lesion / thymine glycol / oxidative thymine lesion / 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 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 / Monooxygenase ...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 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 / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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
DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 2.65 Å
AuthorsAller, P. / Rould, M.A. / Hogg, M. / Wallace, S.S. / Doublie, S.
CitationJournal: 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
DepositionSep 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
F: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
G: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
H: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
I: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
J: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
K: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
L: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
A: DNA polymerase
B: DNA polymerase
C: DNA polymerase
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)463,95712
Polymers463,95712
Non-polymers00
Water10,917606
1
E: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
F: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,9893
Polymers115,9893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-27 kcal/mol
Surface area45260 Å2
MethodPISA
2
G: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
H: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
B: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,9893
Polymers115,9893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-29 kcal/mol
Surface area43720 Å2
MethodPISA
3
I: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
J: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
C: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,9893
Polymers115,9893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-35 kcal/mol
Surface area44230 Å2
MethodPISA
4
K: 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'
L: 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,9893
Polymers115,9893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-27 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.612, 122.632, 168.695
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'


Mass: 5600.620 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'


Mass: 4560.959 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
DNA polymerase / / Gp43


Mass: 105827.570 Da / Num. of mol.: 4 / Mutation: D222A, D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: gp43 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.93 Å3/Da / Density % sol: 57.97 % / Description: the file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG2000 MME, Magnesium Sulfate, Sodium acetate, HEPES buffer pH7.0, Beta-mercaptoethanol, glycerol, 3 cycles of Macro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2sodium acetate11
3magnesium sulfate11
4beta-mercaptoethanol2-Mercaptoethanol11
5water11
6PEG 200012
7sodium acetate12
8magnesium sulfate12
9water12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2005 / Details: MIRRORS
RadiationMonochromator: DCM - PAIR OF FLAT SI CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 324831 / Num. obs: 286985 / % possible obs: 97.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.112 / Χ2: 1.033 / Net I/σ(I): 12.5
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.07 / Num. unique all: 13115 / Χ2: 1.006 / % possible all: 84.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: Isomorphous Replacement
Starting model: 1RV2

1rv2
PDB Unreleased entry


Resolution: 2.65→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.281 27321 8.4 %RANDOM
Rwork0.229 ---
all-324831 --
obs-286985 88.3 %-
Solvent computationBsol: 40.218 Å2
Displacement parametersBiso mean: 67.37 Å2
Baniso -1Baniso -2Baniso -3
1-4.396 Å20 Å2-11.643 Å2
2--1.799 Å20 Å2
3----6.195 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28700 2637 0 606 31943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.246
X-RAY DIFFRACTIONc_mcbond_it1.3941.5
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_mcangle_it2.4242
X-RAY DIFFRACTIONc_scangle_it2.9182.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5hetero-cpds-060110mr.paramhetero-cpds-060110mr.top

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