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- PDB-3wdg: Staphylococcus aureus UDG / UGI complex -

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Basic information

Entry
Database: PDB / ID: 3wdg
TitleStaphylococcus aureus UDG / UGI complex
Components
  • Uncharacterized protein
  • Uracil-DNA glycosylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / uracil-DNA glycosylase / uracil-DNA glycosylase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / metal ion binding / cytoplasm
Similarity search - Function
S. aureus uracil DNA glycosylase inhibitor / S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / 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 ...S. aureus uracil DNA glycosylase inhibitor / S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, H.C. / Ko, T.P. / Wang, A.H.J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor.
Authors: Wang, H.C. / Hsu, K.C. / Yang, J.M. / Wu, M.L. / Ko, T.P. / Lin, S.R. / Wang, A.H.J.
History
DepositionJun 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,4392
Polymers39,4392
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-8 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.602, 86.367, 88.518
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 Uracil-DNA glycosylase / UDG


Mass: 26071.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: ung, SAR0586 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GJ88, uracil-DNA glycosylase
#2: Protein Uncharacterized protein / SAUGI


Mass: 13367.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q936H5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.2
Details: 0.1M Hepes sodium pH7.2, 15% PEG 20000, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: LN2-cooled, fixed-exit double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→61.82 Å / Num. all: 20713 / Num. obs: 20216 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.7
Reflection shellResolution: 2.2→2.28 Å / % possible all: 80.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UGI, 2KCD

2ugi

2kcd


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.734 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1029 5.1 %RANDOM
Rwork0.17109 ---
all0.17367 19658 --
obs0.17367 19068 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.027 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 0 290 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222755
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9483744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59224.745137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.029159
X-RAY DIFFRACTIONr_chiral_restr0.1260.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212107
X-RAY DIFFRACTIONr_mcbond_it0.8421.51631
X-RAY DIFFRACTIONr_mcangle_it1.61122654
X-RAY DIFFRACTIONr_scbond_it2.78831124
X-RAY DIFFRACTIONr_scangle_it4.5814.51090
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 70 -
Rwork0.165 1075 -
obs--76.23 %

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