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- PDB-2dtu: Crystal structure of the beta hairpin loop deletion variant of RB... -

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Basic information

Entry
Database: PDB / ID: 2dtu
TitleCrystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog
Components
  • 5'-D(*CP*GP*(3DR)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'
  • 5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3'
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA POLYMERASE / ABASIC SITE / DNA LESION / BETA HAIRPIN DELETION / 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: 2.37 Å
AuthorsAller, P. / Hogg, M. / Konigsberg, W. / Wallace, S.S. / Doublie, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family.
Authors: Hogg, M. / Aller, P. / Konigsberg, W. / Wallace, S.S. / Doublie, S.
History
DepositionJul 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: 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_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)455,05012
Polymers455,05012
Non-polymers00
Water15,439857
1
E: 5'-D(*CP*GP*(3DR)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'
F: 5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3'
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)113,7633
Polymers113,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*GP*(3DR)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'
H: 5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3'
B: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)113,7633
Polymers113,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: 5'-D(*CP*GP*(3DR)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'
J: 5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3'
C: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)113,7633
Polymers113,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: 5'-D(*CP*GP*(3DR)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'
L: 5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3'
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)113,7633
Polymers113,7633
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.074, 123.061, 164.564
Angle α, β, γ (deg.)90.00, 96.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 5368.457 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3'


Mass: 4634.023 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
DNA polymerase / / Gp43


Mass: 103760.133 Da / Num. of mol.: 4 / Mutation: D222A, D327A, I253G, Deletion 254-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: 43 / 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.: 857 / 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: 58 % / Description: the file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES pH 7.1, glycerol, 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: 2.37→50 Å / Num. all: 396029 / Num. obs: 376279 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.082 / Χ2: 1.051 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.37-2.453.50.41169401.21380.6
2.45-2.553.80.355188341.20989.8
2.55-2.675.30.305205691.18498.1
2.67-2.815.20.235210211.15299.9
2.81-2.995.70.165209981.067100
2.99-3.225.70.114210581.085100
3.22-3.545.60.088210401.032100
3.54-4.055.60.069210670.921100
4.05-5.15.60.066211740.904100
5.1-505.60.071213320.92499.6

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Processing

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

1rv2
PDB Unreleased entry


Resolution: 2.37→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.268 35734 8.5 %RANDOM
Rwork0.223 ---
all-396029 --
obs-376279 89.4 %-
Solvent computationBsol: 45.954 Å2
Displacement parametersBiso mean: 73.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.964 Å20 Å2-10.239 Å2
2--5.92 Å20 Å2
3----6.885 Å2
Refinement stepCycle: LAST / Resolution: 2.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28945 2652 0 857 32454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.195
X-RAY DIFFRACTIONc_mcbond_it1.4111.5
X-RAY DIFFRACTIONc_scbond_it2.0532
X-RAY DIFFRACTIONc_mcangle_it2.3772
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.37→2.45 Å
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

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