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- PDB-3zor: Structure of BsUDG -

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Basic information

Entry
Database: PDB / ID: 3zor
TitleStructure of BsUDG
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsBanos-Sanz, J.I. / Mojardin, L. / Sanz-Aparicio, J. / Gonzalez, B. / Salas, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Crystal Structure and Functional Insights Into Uracil-DNA Glycosylase Inhibition by Phage Phi29 DNA Mimic Protein P56
Authors: Banos-Sanz, J.I. / Mojardin, L. / Sanz-Aparicio, J. / Lazaro, J.M. / Villar, L. / Serrano-Heras, G. / Gonzalez, B. / Salas, M.
History
DepositionFeb 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)26,0841
Polymers26,0841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.305, 79.795, 97.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein URACIL-DNA GLYCOSYLASE / UDG


Mass: 26083.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PT7-4-UDG-WT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39615, uracil-DNA glycosylase

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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: 2.51 Å3/Da / Density % sol: 50.94 % / Description: NONE
Crystal growTemperature: 291 K / pH: 7.5
Details: 0.2 M SODIUM FLUORIDE AND 20% PEG 3350 AT 291 K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→48.98 Å / Num. obs: 5596 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZOQ, CHAIN A

3zoq


Resolution: 2.95→48.73 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.84 / SU B: 24.305 / SU ML: 0.479 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29516 252 4.5 %RANDOM
Rwork0.23779 ---
obs0.24045 5313 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.877 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2---1.96 Å20 Å2
3---4.54 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 0 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9482534
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68423.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10715329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7741514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211442
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 14 -
Rwork0.25 368 -
obs--99.74 %

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