[English] 日本語
Yorodumi
- PDB-6ajr: Complex form of Uracil DNA glycosylase X and uracil -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ajr
TitleComplex form of Uracil DNA glycosylase X and uracil
ComponentsUracil DNA glycosylase superfamily protein
KeywordsDNA BINDING PROTEIN / DNA repair / Base excision / DNA-Protein crosslink.
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function
Uracil-DNA glycosylase family 4 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / URACIL / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.341 Å
AuthorsAhn, W.C. / Aroli, S. / Varshney, U. / Woo, E.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1A2A2A05021648 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.
Authors: Ahn, W.C. / Aroli, S. / Kim, J.H. / Moon, J.H. / Lee, G.S. / Lee, M.H. / Sang, P.B. / Oh, B.H. / Varshney, U. / Woo, E.J.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil DNA glycosylase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6653
Polymers22,2011
Non-polymers4642
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-20 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.479, 51.773, 55.107
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uracil DNA glycosylase superfamily protein


Mass: 22201.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_0265 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QP43
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-URA / URACIL / Uracil


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 2.0M ammonium citrate tribasic pH7.0, 0.1M Bis-Tris propane pH7.0

-
Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 43403 / % possible obs: 97.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 54.35
Reflection shellResolution: 1.34→1.36 Å / Rmerge(I) obs: 0.238 / Num. unique obs: 2162

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.341→19.008 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.7
RfactorNum. reflection% reflection
Rfree0.1657 2010 4.63 %
Rwork0.1384 --
obs0.1397 43379 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.341→19.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 16 299 1837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071579
X-RAY DIFFRACTIONf_angle_d0.892146
X-RAY DIFFRACTIONf_dihedral_angle_d8.835917
X-RAY DIFFRACTIONf_chiral_restr0.075241
X-RAY DIFFRACTIONf_plane_restr0.006282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3413-1.37480.19681390.14272932X-RAY DIFFRACTION97
1.3748-1.4120.15861420.13223013X-RAY DIFFRACTION100
1.412-1.45350.17011550.12712995X-RAY DIFFRACTION100
1.4535-1.50040.16271390.11843002X-RAY DIFFRACTION100
1.5004-1.5540.17021510.11613010X-RAY DIFFRACTION100
1.554-1.61620.16291380.11133038X-RAY DIFFRACTION100
1.6162-1.68970.14621460.11523026X-RAY DIFFRACTION100
1.6897-1.77870.13621660.11542991X-RAY DIFFRACTION100
1.7787-1.89010.14521280.11643059X-RAY DIFFRACTION100
1.8901-2.03590.14781520.12093025X-RAY DIFFRACTION100
2.0359-2.24050.15121440.12883024X-RAY DIFFRACTION100
2.2405-2.5640.16211520.13773020X-RAY DIFFRACTION100
2.564-3.22780.15841520.15893031X-RAY DIFFRACTION99
3.2278-19.00950.23511060.18452203X-RAY DIFFRACTION71

+
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