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- PDB-8e9a: Crystal structure of AsfvPolX in complex with 10-23 DNAzyme and Mg -

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Basic information

Entry
Database: PDB / ID: 8e9a
TitleCrystal structure of AsfvPolX in complex with 10-23 DNAzyme and Mg
Components
  • DNA/RNA (52-MER)
  • Repair DNA polymerase X
KeywordsTRANSFERASE/DNA / DNAzyme / DNA / TRANSFERASE-DNA complex
Function / homology
Function and homology information


double-strand break repair via nonhomologous end joining / virion component / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding
Similarity search - Function
Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus BA71V
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsCramer, E.R. / Robart, A.R. / Kaya, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM133857 United States
CitationJournal: Commun Chem / Year: 2023
Title: Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation.
Authors: Cramer, E.R. / Starcovic, S.A. / Avey, R.M. / Kaya, A.I. / Robart, A.R.
History
DepositionAug 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repair DNA polymerase X
B: Repair DNA polymerase X
C: DNA/RNA (52-MER)
D: DNA/RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,50422
Polymers73,0824
Non-polymers42218
Water57632
1
A: Repair DNA polymerase X
C: DNA/RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,75011
Polymers36,5412
Non-polymers2109
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Repair DNA polymerase X
D: DNA/RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,75311
Polymers36,5412
Non-polymers2129
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.829, 48.419, 139.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Repair DNA polymerase X / Pol X / AsfvPolX


Mass: 20438.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Strain: Badajoz 1971 Vero-adapted / Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase
#2: DNA chain DNA/RNA (52-MER)


Mass: 16102.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M HEPES (pH 7.5), and 25% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 11, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→139.85 Å / Num. obs: 21227 / % possible obs: 97.53 % / Redundancy: 3.4 % / Biso Wilson estimate: 74.42 Å2 / CC1/2: 0.977 / Net I/σ(I): 2.1
Reflection shellResolution: 2.69→2.82 Å / Num. unique obs: 2818 / CC1/2: 0.305 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XM8

5xm8


Resolution: 2.69→69.92 Å / SU ML: 0.478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2886 1035 4.88 %
Rwork0.255 20191 -
obs0.2566 21226 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.84 Å2
Refinement stepCycle: LAST / Resolution: 2.69→69.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 18 32 4932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01075179
X-RAY DIFFRACTIONf_angle_d1.15927395
X-RAY DIFFRACTIONf_chiral_restr0.0495846
X-RAY DIFFRACTIONf_plane_restr0.0062572
X-RAY DIFFRACTIONf_dihedral_angle_d27.95942104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.830.38211320.37492519X-RAY DIFFRACTION86.41
2.83-3.010.35381600.3472823X-RAY DIFFRACTION97.8
3.01-3.240.35641660.31982917X-RAY DIFFRACTION99.94
3.24-3.570.30981440.25792936X-RAY DIFFRACTION99.84
3.57-4.080.29581540.26492943X-RAY DIFFRACTION99.74
4.08-5.140.27411340.23512980X-RAY DIFFRACTION99.27
5.15-69.920.24911450.22143073X-RAY DIFFRACTION99.6

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