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- PDB-2j8x: Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi fro... -

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Basic information

Entry
Database: PDB / ID: 2j8x
TitleEpstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2
Components
  • URACIL-DNA GLYCOSYLASE
  • URACIL-DNA GLYCOSYLASE INHIBITOR
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / EBV / DNA REPAIR / LYTIC PROTEIN / EPSTEIN-BARR VIRUS / URACIL- DNA GLYCOSYLASE / HYDROLASE / URACIL-DNA GLYCOSYLASE INHIBITOR
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / host cell nucleus
Similarity search - Function
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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
UREA / Uracil-DNA glycosylase / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesEPSTEIN-BARR VIRUS (Epstein-Barr virus)
BACILLUS PHAGE PBS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGeoui, T. / Buisson, M. / Tarbouriech, N. / Burmeister, W.P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: New Insights on the Role of the Gamma-Herpesvirus Uracil-DNA Glycosylase Leucine Loop Revealed by the Structure of the Epstein-Barr Virus Enzyme in Complex with an Inhibitor Protein.
Authors: Geoui, T. / Buisson, M. / Tarbouriech, N. / Burmeister, W.P.
History
DepositionOct 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,6036
Polymers70,4834
Non-polymers1202
Water7,008389
1
A: URACIL-DNA GLYCOSYLASE
B: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3013
Polymers35,2412
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-12 kcal/mol
Surface area13780 Å2
MethodPISA
2
C: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3013
Polymers35,2412
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-11 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.406, 82.942, 269.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.896536, -0.04962, -0.440184), (0.141372, -0.909691, 0.390482), (-0.419807, -0.412311, -0.808555)34.376, 8.332, 193.96
2given(0.881249, -0.07454, -0.466737), (0.145511, -0.896739, 0.417953), (-0.449696, -0.436236, -0.779404)38.474, 4.517, 191.553

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Components

#1: Protein URACIL-DNA GLYCOSYLASE


Mass: 25758.666 Da / Num. of mol.: 2 / Fragment: URACIL-DNA GLYCOSYLASE DOMAIN, RESIDUES 25-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EPSTEIN-BARR VIRUS (Epstein-Barr virus)
Strain: B95-8 / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q777D9, UniProt: P12888*PLUS, uridine nucleosidase
#2: Protein URACIL-DNA GLYCOSYLASE INHIBITOR


Mass: 9482.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE PBS2 (virus) / Strain: PBS-2 / Plasmid: PRSETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14739
#3: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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 %
Description: E.COLI UNG-UGI COMPLEX USED FOR MOLECULAR REPLACEMENT.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION METHOD. PROTEIN IN 100 MM NACL, 20 MM TRIS-HCL PH 7.5 AND 10 MM DTT AT 30 TO 50 MG/ML. RESERVOIR SOLUTION OF 20% PEG 3350 AND 0.05 M NH4CL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: CHANNEL-CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→67.3 Å / Num. obs: 29123 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 5.81 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.84 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.16 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LQM

1lqm


Resolution: 2.3→49.88 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.563 / SU ML: 0.181 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1482 5.1 %RANDOM
Rwork0.193 ---
obs0.196 27583 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 8 389 5307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0225032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8291.9666839
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7485619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58424.955222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56115864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4981522
X-RAY DIFFRACTIONr_chiral_restr0.060.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22392
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23387
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2417
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.16933187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.30245033
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38222087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.18631806
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 112
Rwork0.214 1954
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42610.010.20940.5186-0.03910.6164-0.0109-0.0263-0.04330.0050.0216-0.0510.0256-0.0157-0.0107-0.0193-0.00910.0041-0.04380.0028-0.01341.902519.9616119.2076
20.8462-0.3719-0.40120.7867-0.28781.74350.052-0.0321-0.0049-0.03650.0594-0.0521-0.13960.027-0.1114-0.0031-0.04670.0121-0.0454-0.0305-0.01958.866742.0522117.1613
31.9152-0.09790.50310.6684-0.6751.1785-0.16330.37270.21460.08980.014-0.0012-0.0111-0.00820.1494-0.0293-0.0249-0.0706-0.00230.0507-0.0492-17.395736.891488.6013
42.9976-0.3970.22372.7215-0.11391.61990.30140.8086-0.4081-0.0616-0.1390.19440.19320.5034-0.1624-0.02530.0516-0.06030.1904-0.1739-0.1184-11.520816.932978.2506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 255
2X-RAY DIFFRACTION2B2 - 84
3X-RAY DIFFRACTION3C27 - 255
4X-RAY DIFFRACTION4D4 - 84

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