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- PDB-5ays: Crystal structure of SAUGI/HSV UDG complex -

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Basic information

Entry
Database: PDB / ID: 5ays
TitleCrystal structure of SAUGI/HSV UDG complex
Components
  • Uncharacterized protein
  • Uracil-DNA glycosylase
KeywordsHYDROLASE INHIBITOR / DNA mimic protein / DNA mimicking / uracil-DNA glycosylase inhibitor / uracil-DNA glycosylase / Herpes simplex virus
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / host cell nucleus / metal ion binding
Similarity search - Function
S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / 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 / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / 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 speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWang, H.C. / Ko, T.P. / Huang, M.F. / Wang, A.H.J.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
National Science CouncilNSC 102-2311-B-038 -003 Taiwan
National Science CouncilMOST 103-2311-B-038 -005 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase.
Authors: Wang, H.C. / Ho, C.H. / Chou, C.C. / Ko, T.P. / Huang, M.F. / Hsu, K.C. / Wang, A.H.
History
DepositionSep 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,5794
Polymers84,5794
Non-polymers00
Water12,827712
1
A: Uracil-DNA glycosylase
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)42,2892
Polymers42,2892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-7 kcal/mol
Surface area15490 Å2
MethodPISA
2
B: Uracil-DNA glycosylase
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)42,2892
Polymers42,2892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.298, 63.010, 65.512
Angle α, β, γ (deg.)65.10, 89.58, 88.38
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13C
23D
14C
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A10 - 52
2111B10 - 52
1211A54 - 59
2211B54 - 59
1311A61 - 86
2311B61 - 86
1411A88 - 153
2411B88 - 153
1511A155 - 250
2511B155 - 250
1125A50 - 90
2125B50 - 90
1225A150 - 160
2225B150 - 160
1135C10 - 40
2135D10 - 40
1141C1 - 18
2141D1 - 18
1241C20 - 29
2241D20 - 29
1341C31 - 110
2341D31 - 110

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Uracil-DNA glycosylase / UDG / UNG


Mass: 28922.137 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 91-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10186, uracil-DNA glycosylase
#2: Protein Uncharacterized protein / SAUGI


Mass: 13367.123 Da / Num. of mol.: 2
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.: 712 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→20 Å / Num. obs: 41236 / % possible obs: 95.6 % / Redundancy: 2.1 % / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
Blu-Icedata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAU, 3WDG

1lau

3wdg


Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.807 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22253 2191 5 %RANDOM
Rwork0.19486 ---
obs0.19629 41236 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.903 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20.1 Å20.22 Å2
2--3.66 Å2-1.3 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.09→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5520 0 0 712 6232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9537748
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6195674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72622.701274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09815914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.211550
X-RAY DIFFRACTIONr_chiral_restr0.1180.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0214386
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_it2.9761.53404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3142.55536
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7372.52276
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7663.52212
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1798tight positional0.090.05
11B1798tight thermal2.3550
22A208medium positional0.120.5
22B215loose positional0.385
22A208medium thermal1.87
22B215loose thermal4
31C124medium positional0.060.5
31D139loose positional0.295
31C124medium thermal2.15
31D139loose thermal3
42C907tight positional0.060.05
42D907tight thermal2.2250
LS refinement shellResolution: 2.086→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 117 -
Rwork0.265 2632 -
obs--80.9 %

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