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- PDB-2p5g: Crystal structure of RB69 gp43 in complex with DNA with dAMP oppo... -

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Basic information

Entry
Database: PDB / ID: 2p5g
TitleCrystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template
Components
  • DNA polymerase
  • Primer DNA
  • Template DNA
Keywordstransferase/DNA / DNA POLYMERASE / ABASIC SITE / DNA LESION / dAMP / 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: 2.8 Å
AuthorsZahn, K.E. / Belrhali, H. / Wallace, S.S. / Doublie, S.
CitationJournal: Biochemistry / Year: 2007
Title: Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide.
Authors: Zahn, K.E. / Belrhali, H. / Wallace, S.S. / Doublie, S.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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: 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)467,04712
Polymers467,04712
Non-polymers00
Water7,260403
1
E: Template DNA
F: Primer DNA
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)116,7623
Polymers116,7623
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)116,7623
Polymers116,7623
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)116,7623
Polymers116,7623
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)116,7623
Polymers116,7623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.628, 122.272, 163.871
Angle α, β, γ (deg.)90.00, 96.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
Template DNA


Mass: 6300.051 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
Primer DNA


Mass: 4634.023 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: 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.: 403 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000 MME11
2sodium acetate11
3magnesium sulfate11
4beta-mercaptoethanol2-Mercaptoethanol11
5PEG 2000 MME12
6sodium acetate12
7magnesium sulfate12

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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 3, 2006 / 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: 2.8→50 Å / Num. all: 125168 / Num. obs: 125168 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.6 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0011refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: Isomorphous Replacement
Starting model: 1RV2

1rv2
PDB Unreleased entry


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU B: 16.636 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29524 10837 9.6 %RANDOM
Rwork0.23422 ---
obs0.24013 101465 88.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 73.922 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å23.35 Å2
2---1.66 Å20 Å2
3---2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26440 2336 0 403 29179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02229684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0622.05740758
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04253393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23824.1371252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.767154295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.38115146
X-RAY DIFFRACTIONr_chiral_restr0.070.24416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0222141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.214415
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.220209
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.21220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.2183
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4771.517323
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.788227070
X-RAY DIFFRACTIONr_scbond_it0.902314988
X-RAY DIFFRACTIONr_scangle_it1.4844.513688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 550 -
Rwork0.305 5379 -
obs--64.03 %

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