[English] 日本語
Yorodumi
- PDB-2ugi: PROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THE URACIL GLYC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ugi
TitlePROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THE URACIL GLYCOSYLASE INHIBITOR PROTEIN AND ITS COMPLEX WITH ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE INHIBITOR
KeywordsHYDROLASE INHIBITOR / PROTEIN MIMICRY OF DNA / PROTEIN INHIBITOR
Function / homologyBacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / IMIDAZOLE / Uracil-DNA glycosylase inhibitor
Function and homology information
Biological speciesBacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPutnam, C.D. / Arvai, A.S. / Mol, C.D. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase
Authors: Putnam, C.D. / Shroyer, M.J. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
History
DepositionNov 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,0343
Polymers18,9652
Non-polymers691
Water1,27971
1
A: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5522
Polymers9,4831
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)9,4831
Polymers9,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.092, 59.387, 73.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35163, 0.01929, 0.93594), (-0.00942, -0.99981, 0.01707), (0.93609, -0.00282, 0.35175)
Vector: 14.17055, 37.25146, -9.82261)

-
Components

#1: Protein URACIL-DNA GLYCOSYLASE INHIBITOR / UGI


Mass: 9482.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBS2 (virus) / Cellular location: CYTOPLASM / Plasmid: PZWTAC1 / Cellular location (production host): CYTOPLASM / Gene (production host): TAC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P14739
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / pH: 8.2
Details: (NH4)2SO4, IMIDAZOLE, MALATE, (NH4)2SO4, pH 8.2, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2IMIDAZOLE11
3MALATE11
4(NH4)2SO412
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
184 %satammonium sulfate1reservoir
2200 mMimidazole/malate1reservoir
31
41

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 9507 / % possible obs: 95.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.2 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6.2 / Rsym value: 0.251 / % possible all: 91.8
Reflection
*PLUS
Num. obs: 9493 / % possible obs: 95.3 % / Num. measured all: 34065 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 91.9 % / Num. unique obs: 883 / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8.5

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UGI FROM THE HUMAN UDG:UGI CRYSTAL STRUCTURE

Resolution: 2.2→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 958 10 %RANDOM
Rwork0.227 ---
all-9435 --
obs-9435 96.1 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--8.34 Å20 Å20 Å2
2--5.643 Å20 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 5 71 1384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.556
X-RAY DIFFRACTIONx_mcangle_it2.724
X-RAY DIFFRACTIONx_scbond_it2.417
X-RAY DIFFRACTIONx_scangle_it3.888
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.363 95 8 %
Rwork0.362 1081 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25
LS refinement shell
*PLUS
Rfactor obs: 0.362

+
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