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- PDB-2p5o: Crystal structure of RB69 GP43 in complex with DNA containing an ... -

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Basic information

Entry
Database: PDB / ID: 2p5o
TitleCrystal structure of RB69 GP43 in complex with DNA containing an abasic site analog
Components
  • DNA polymerase
  • Primer DNA
  • Template DNA
Keywordstransferase/DNA / DNA POLYMERASE / ABASIC SITE / DNA LESION / EXONUCLEASE SWITCH / transferase-DNA COMPLEX
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / 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 / MAD / Resolution: 2.8 Å
AuthorsHogg, M. / Wallace, S.S. / Doublie, S.
CitationJournal: Embo J. / Year: 2004
Title: Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
Authors: Hogg, M. / Wallace, S.S. / Doublie, S.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionApr 3, 2007ID: 1RV2
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Oct 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Template DNA
F: Primer DNA
G: Template DNA
H: Primer DNA
I: Template DNA
J: Primer DNA
K: Template DNA
L: Primer DNA
A: DNA polymerase
B: DNA polymerase
C: DNA polymerase
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)463,32012
Polymers463,32012
Non-polymers00
Water8,917495
1
E: Template DNA
F: Primer DNA
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,8303
Polymers115,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Template DNA
H: Primer DNA
B: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,8303
Polymers115,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Template DNA
J: Primer DNA
C: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,8303
Polymers115,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: Template DNA
L: Primer DNA
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,8303
Polymers115,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.018, 123.209, 165.616
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
Template DNA


Mass: 5368.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Commercially produced
#2: DNA chain
Primer DNA


Mass: 4634.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Commercially produced
#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: 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


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 2000 MME. 100mM Magnesium sulfate, 100mM HEPES, 100mM Sodium acetate, 15% glycerol, 2mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2Magnesium sulfate11
3Sodium acetate11
4HEPES11
5glycerol11
6BME11
7PEG 200012
8Magnesium sulfate12
9Sodium acetate12
10HEPES12
11glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9500, 0.9788, 0.9790
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Aug 5, 2002 / Details: Double crystal monochromator
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97881
30.9791
ReflectionResolution: 2.8→44 Å / Num. all: 257534 / Num. obs: 234220 / % possible obs: 90.9 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.93 Å / % possible all: 98.7

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 22643 -random
Rwork0.245 ---
all-257534 --
obs-234220 90.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25015 2242 0 495 27752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3074
X-RAY DIFFRACTIONc_bond_d0.007856
X-RAY DIFFRACTIONc_mcangle_it2.314
X-RAY DIFFRACTIONc_mcbond_it1.324
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0.014 /
RfactorNum. reflection
Rfree0.434 1017
Rwork0.379 -

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