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- PDB-4i9l: Crystal structure of the D714A mutant of RB69 DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 4i9l
TitleCrystal structure of the D714A mutant of RB69 DNA polymerase
ComponentsDNA polymerase
KeywordsHYDROLASE / TRANSFERASE / PALM SUBDOMAIN
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 / : ...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 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 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
GUANOSINE / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJacewicz, A. / Trzemecka, A. / Guja, K.E. / Plochocka, D. / Yakubovskaya, E. / Bebenek, A. / Garcia-Diaz, M.
CitationJournal: Plos One / Year: 2013
Title: A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site.
Authors: Jacewicz, A. / Trzemecka, A. / Guja, K.E. / Plochocka, D. / Yakubovskaya, E. / Bebenek, A. / Garcia-Diaz, M.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2898
Polymers104,6111
Non-polymers6787
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.875, 199.369, 80.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase / Gp43


Mass: 104611.133 Da / Num. of mol.: 1 / Mutation: D222A, D327A, D714A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 4.5 Å3/Da / Density % sol: 72.67 %
Crystal growpH: 5.6
Details: 1.65 M AMMONIUM SULPHATE, 0.01 M MAGNESIUM CHLORIDE, 0.05 M SODIUM CITRATE DIHYDROGEN, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 59560 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.829 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IH7

1ih7


Resolution: 2.6→33.24 Å / SU ML: 2.1 / σ(F): 0.09 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1732 3.32 %
Rwork0.214 --
obs0.216 52147 86.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.11 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5895 Å20 Å2-0 Å2
2--7.7354 Å2-0 Å2
3----6.1459 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 38 220 7626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087601
X-RAY DIFFRACTIONf_angle_d1.01610280
X-RAY DIFFRACTIONf_dihedral_angle_d16.8062817
X-RAY DIFFRACTIONf_chiral_restr0.0681082
X-RAY DIFFRACTIONf_plane_restr0.0051325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.65810.37441080.313190X-RAY DIFFRACTION67
2.6581-2.74390.38481200.30463617X-RAY DIFFRACTION76
2.7439-2.84190.33881250.30143863X-RAY DIFFRACTION80
2.8419-2.95560.34011290.28613876X-RAY DIFFRACTION82
2.9556-3.090.281400.2744147X-RAY DIFFRACTION86
3.09-3.25280.31451470.26994201X-RAY DIFFRACTION87
3.2528-3.45640.28711450.25264090X-RAY DIFFRACTION85
3.4564-3.7230.29921540.22334340X-RAY DIFFRACTION90
3.723-4.0970.22851570.19124529X-RAY DIFFRACTION94
4.097-4.68840.20421640.15724699X-RAY DIFFRACTION96
4.6884-5.90160.18781700.16934855X-RAY DIFFRACTION99
5.9016-33.24050.21381730.19965008X-RAY DIFFRACTION98

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