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- PDB-5x55: Crystal structure of mimivirus uracil-DNA glycosylase -

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Basic information

Entry
Database: PDB / ID: 5x55
TitleCrystal structure of mimivirus uracil-DNA glycosylase
ComponentsProbable uracil-DNA glycosylase
KeywordsHYDROLASE / Family-I uracil-DNA glycosylase / long N-domain / insertional motif
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / base-excision repair
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
Probable uracil-DNA glycosylase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsKwon, E. / Pathak, D. / Kim, D.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)2014R1A4A1071040 Korea, Republic Of
National Research Foundation of Korea (NRF)2014R1A1A1002064 Korea, Republic Of
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure of mimivirus uracil-DNA glycosylase
Authors: Kwon, E. / Pathak, D. / Chang, H.W. / Kim, D.Y.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable uracil-DNA glycosylase
B: Probable uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)84,5542
Polymers84,5542
Non-polymers00
Water5,765320
1
A: Probable uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)42,2771
Polymers42,2771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)42,2771
Polymers42,2771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.267, 95.618, 132.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable uracil-DNA glycosylase / UDG


Mass: 42276.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: UNG, MIMI_L249 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5UPT2, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1.8 Å3/Da / Density % sol: 31.72 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5 / Details: HEPES, PEG3350, Isopropanol, CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 27418 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.047 / Net I/σ(I): 26.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2313: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CXM

3cxm


Resolution: 2.302→29.744 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.86
RfactorNum. reflection% reflection
Rfree0.2156 1376 5.03 %
Rwork0.1731 --
obs0.1753 27381 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.302→29.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 0 320 4814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084643
X-RAY DIFFRACTIONf_angle_d0.9876318
X-RAY DIFFRACTIONf_dihedral_angle_d12.6092759
X-RAY DIFFRACTIONf_chiral_restr0.057676
X-RAY DIFFRACTIONf_plane_restr0.006796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3016-2.38380.26521580.21052508X-RAY DIFFRACTION98
2.3838-2.47920.2965940.20592617X-RAY DIFFRACTION100
2.4792-2.59190.23471300.2032585X-RAY DIFFRACTION100
2.5919-2.72850.2431510.19572564X-RAY DIFFRACTION100
2.7285-2.89930.25871540.19372549X-RAY DIFFRACTION100
2.8993-3.1230.25141170.19392603X-RAY DIFFRACTION100
3.123-3.43680.26121430.18222615X-RAY DIFFRACTION100
3.4368-3.93320.1971270.15592613X-RAY DIFFRACTION100
3.9332-4.95170.14721390.13852648X-RAY DIFFRACTION100
4.9517-29.74680.19421630.15852703X-RAY DIFFRACTION100

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