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- PDB-3wdf: Staphylococcus aureus UDG -

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Basic information

Entry
Database: PDB / ID: 3wdf
TitleStaphylococcus aureus UDG
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / Uracil-DNA glycosylase
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / cytoplasm
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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 speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)52,1432
Polymers52,1432
Non-polymers00
Water9,314517
1
A: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)26,0711
Polymers26,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)26,0711
Polymers26,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.408, 79.494, 62.627
Angle α, β, γ (deg.)90.00, 112.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 1 - 216 / Label seq-ID: 1 - 216

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Uracil-DNA glycosylase / / UDG


Mass: 26071.443 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 50.71 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.1M Hepes sodium pH7.5, 10% 2-propanol, 18% PEG 4000 , 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: Jul 5, 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: 1.48→58.04 Å / Num. all: 84916 / Num. obs: 82029 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.5
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 4.1 % / % possible all: 94.7

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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: 2JHQ

2jhq


Resolution: 1.48→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.531 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19232 4104 5 %RANDOM
Rwork0.1464 ---
all0.14872 80818 --
obs0.14872 77860 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-1.33 Å2
2--0.15 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 0 517 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223608
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9344902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30724.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40615602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3481514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212772
X-RAY DIFFRACTIONr_mcbond_it2.0341.52162
X-RAY DIFFRACTIONr_mcangle_it3.21123516
X-RAY DIFFRACTIONr_scbond_it4.63631446
X-RAY DIFFRACTIONr_scangle_it6.9224.51386
X-RAY DIFFRACTIONr_rigid_bond_restr2.28733608
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A864medium positional0.20.5
A887loose positional0.475
B864medium thermal1.162
B887loose thermal1.4810
LS refinement shellResolution: 1.481→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 269 -
Rwork0.236 5458 -
obs--91.75 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
116.146832.764722.6791
25.1105-0.52353.3191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 216
2X-RAY DIFFRACTION2B1 - 216

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