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- PDB-2c2p: The crystal structure of mismatch specific uracil-DNA glycosylase... -

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Basic information

Entry
Database: PDB / ID: 2c2p
TitleThe crystal structure of mismatch specific uracil-DNA glycosylase (MUG) from Deinococcus radiodurans
ComponentsG/U MISMATCH-SPECIFIC DNA GLYCOSYLASE
KeywordsHYDROLASE / DEINOCOCCUS RADIODURANS / RADIATION RESISTANCE / DNA REPAIR ENZYMES / URACIL-DNA GLYCOSYLASE / MISMATCH SPECIFIC DNA-GLYCOSYLASE / MUG
Function / homology
Function and homology information


pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / uracil DNA N-glycosylase activity
Similarity search - Function
Uracil DNA glycosylase family 2 / 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
ACETATE ION / G/U mismatch-specific DNA glycosylase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMoe, E. / Leiros, I. / Smalas, A.O. / McSweeney, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Crystal Structure of Mismatch Specific Uracil-DNA Glycosylase (Mug) from Deinococcus Radiodurans Reveals a Novel Catalytic Residue and Broad Substrate Specificity
Authors: Moe, E. / Leiros, I. / Smalas, A.O. / Mcsweeney, S.
History
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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: G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8452
Polymers21,7861
Non-polymers591
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.733, 101.733, 37.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-2072-

HOH

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Components

#1: Protein G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE / MISMATCH-SPECIFIC URACIL-DNA GLYCOSYLASE


Mass: 21785.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACETATE BOUND IN THE SUBSTRATE POCKET
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RWF4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.6 Å3/Da / Density % sol: 51.8 %
Crystal growpH: 6.5
Details: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30% W/V PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939272
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939272 Å / Relative weight: 1
ReflectionResolution: 1.75→12 Å / Num. obs: 22686 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.8
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MUG

1mug


Resolution: 1.75→87.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.32 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6 AND 190-199 WERE DISORDERED AND THEREFORE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2071 9.1 %RANDOM
Rwork0.179 ---
obs0.183 20611 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.75→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 4 152 1582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211473
X-RAY DIFFRACTIONr_bond_other_d0.0020.021350
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.9692017
X-RAY DIFFRACTIONr_angle_other_deg1.04733130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021646
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02300
X-RAY DIFFRACTIONr_nbd_refined0.230.2311
X-RAY DIFFRACTIONr_nbd_other0.2540.21564
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.2815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3411.5920
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29821482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1833553
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0344.5535
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: 1.75→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 144
Rwork0.279 1504

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