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- PDB-2oyq: Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP op... -

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Basic information

Entry
Database: PDB / ID: 2oyq
TitleCrystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog
Components
  • DNA polymerase
  • Primer DNA
  • Template DNA
Keywordstransferase/DNA / DNA POLYMERASE / ABASIC SITE / DNA LESION / NUCLEOTIDE BINDING / 5-NITP / 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
Chem-N5P / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 2.86 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
DepositionFeb 22, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,58618
Polymers462,46512
Non-polymers2,1216
Water11,728651
1
E: Template DNA
F: Primer DNA
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6535
Polymers115,6163
Non-polymers1,0362
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)115,6163
Polymers115,6163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Template DNA
J: Primer DNA
C: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6776
Polymers115,6163
Non-polymers1,0613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: Template DNA
L: Primer DNA
D: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6414
Polymers115,6163
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.590, 123.478, 164.331
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 8 molecules EGIKFHJL

#1: DNA chain
Template DNA


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


Mass: 4661.042 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#3: Protein
DNA polymerase / Gp43


Mass: 104655.141 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

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Non-polymers , 3 types, 657 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-N5P / 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE / 5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE


Mass: 518.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2sodium acetate11
3magnesium sulfate11
4beta-mercaptoethanol11
5HEPES11
6glycerol11
7PEG 200012
8sodium acetate12
9magnesium sulfate12
10HEPES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.99187 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: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.86→30 Å / Num. all: 121231 / Num. obs: 121231 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.7
Reflection shellResolution: 2.86→2.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

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

1rv2
PDB Unreleased entry


Resolution: 2.86→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2942 10779 9.7 %RANDOM
Rwork0.22771 ---
obs0.23416 100166 91.18 %-
all-121231 --
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: 74.755 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å22.71 Å2
2---1.98 Å20 Å2
3---3.57 Å2
Refinement stepCycle: LAST / Resolution: 2.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25760 2348 130 651 28889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02229149
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1012.06240068
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10153289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24624.1441226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.914154216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46715141
X-RAY DIFFRACTIONr_chiral_restr0.0710.24323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221649
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.214133
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.219745
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.2178
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4011.516465
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.747226308
X-RAY DIFFRACTIONr_scbond_it0.84312684
X-RAY DIFFRACTIONr_scangle_it1.4974.513748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 615 -
Rwork0.312 5510 -
obs--68.62 %

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