[English] 日本語
Yorodumi
- PDB-2j8x: Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi fro... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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 ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more