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- PDB-3zoq: Structure of BsUDG-p56 complex -

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Basic information

Entry
Database: PDB / ID: 3zoq
TitleStructure of BsUDG-p56 complex
Components
  • P56
  • URACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE/VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / biological process involved in interaction with host / uracil DNA N-glycosylase activity / cytoplasm
Similarity search - Function
Double Stranded RNA Binding Domain - #30 / : / : / Phage phi29, UDG inhibitor P56 / Double Stranded RNA Binding Domain / 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. ...Double Stranded RNA Binding Domain - #30 / : / : / Phage phi29, UDG inhibitor P56 / Double Stranded RNA Binding Domain / 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 / Other non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Protein p56
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
BACILLUS PHAGE PHI29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: Atomic model / Database references
Revision 1.3Mar 6, 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
B: P56
C: P56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3545
Polymers39,2263
Non-polymers1282
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-19 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.770, 66.270, 102.280
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: 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
#2: Protein P56 / LEFT END OF BACTERIOPHAGE PHI-29 CODING FOR 15 POTENTIAL PROTEINS AMONG THESE ARE THE TERMINAL ...LEFT END OF BACTERIOPHAGE PHI-29 CODING FOR 15 POTENTIAL PROTEINS AMONG THESE ARE THE TERMINAL PROTEIN AND THE PROTEINS ENCODED BY THE GENES 1 / 2 (SUS) / 3 / AND (PROBABLY) 4


Mass: 6571.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE PHI29 (virus) / Plasmid: PT7-3-P56-F29 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38503
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.52 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.5
Details: 19% PEG 8000, 0.1 M TRIS-HCL, PH 8.5, 0.25 M MAGNESIUM CHLORIDE AT 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2011 / Details: PT COATED SI MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.45→23.86 Å / Num. obs: 65433 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EUG

2eug


Resolution: 1.45→55.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.026 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18157 3309 5.1 %RANDOM
Rwork0.13937 ---
obs0.14146 61997 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.093 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.2 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.45→55.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 7 484 3148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022979
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9624066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32524.367158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0941520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212359
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_restr1.61532979
X-RAY DIFFRACTIONr_sphericity_free26.9735102
X-RAY DIFFRACTIONr_sphericity_bonded14.88353269
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 231 -
Rwork0.159 4217 -
obs--99.35 %

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