[English] 日本語
Yorodumi
- PDB-5gnw: Crystal structure of Uracil DNA glycosylase-Uracil complex from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gnw
TitleCrystal structure of Uracil DNA glycosylase-Uracil complex from Bradyrhizobium diazoefficiens.
ComponentsBlr0248 protein
KeywordsHYDROLASE / Uracil DNA glycosylase (UDG) / Bradyrhizobium diazoefficiens / DNA repair
Function / homologyUracil-DNA glycosylase-like domain superfamily / URACIL / Blr0248 protein
Function and homology information
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.869 Å
AuthorsPatil, V.V. / Chembazhi, U.V. / Varshney, U. / Woo, E.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity
Authors: Chembazhi, U.V. / Patil, V.V. / Sah, S. / Reeve, W. / Tiwari, R.P. / Woo, E. / Varshney, U.
History
DepositionJul 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Blr0248 protein
D: Blr0248 protein
E: Blr0248 protein
F: Blr0248 protein
A: Blr0248 protein
B: Blr0248 protein
G: Blr0248 protein
H: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,57916
Polymers239,6828
Non-polymers8978
Water00
1
C: Blr0248 protein
D: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1454
Polymers59,9212
Non-polymers2242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-22 kcal/mol
Surface area22760 Å2
MethodPISA
2
E: Blr0248 protein
F: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1454
Polymers59,9212
Non-polymers2242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-22 kcal/mol
Surface area22680 Å2
MethodPISA
3
A: Blr0248 protein
B: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1454
Polymers59,9212
Non-polymers2242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-21 kcal/mol
Surface area22920 Å2
MethodPISA
4
G: Blr0248 protein
H: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1454
Polymers59,9212
Non-polymers2242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-23 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.537, 89.633, 143.780
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Blr0248 protein / Uracil DNA glycosylase


Mass: 29960.271 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Strain: USDA 110 / Gene: blr0248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89XR0
#2: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H4N2O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG3350, 200 mM sodium citrate, 100 mM sodium citrate/citric acid

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.869→29.62 Å / Num. obs: 50661 / % possible obs: 83.2 % / Redundancy: 2.7 % / Net I/σ(I): 2.06
Reflection shellResolution: 2.88→2.93 Å

-
Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 2.869→29.624 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3018 1998 3.94 %
Rwork0.2508 --
obs0.2528 50661 83.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.869→29.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16792 0 64 0 16856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417336
X-RAY DIFFRACTIONf_angle_d0.89723632
X-RAY DIFFRACTIONf_dihedral_angle_d10.8066192
X-RAY DIFFRACTIONf_chiral_restr0.0352536
X-RAY DIFFRACTIONf_plane_restr0.0053064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.869-2.94070.39161270.30283095X-RAY DIFFRACTION75
2.9407-3.02010.37591440.29823503X-RAY DIFFRACTION84
3.0201-3.10890.35911440.28363524X-RAY DIFFRACTION85
3.1089-3.20910.38821440.28373531X-RAY DIFFRACTION85
3.2091-3.32370.3411440.2763478X-RAY DIFFRACTION84
3.3237-3.45660.29721450.26843551X-RAY DIFFRACTION85
3.4566-3.61360.31851430.27293490X-RAY DIFFRACTION84
3.6136-3.80380.35021430.2633494X-RAY DIFFRACTION84
3.8038-4.04150.26781450.22883510X-RAY DIFFRACTION84
4.0415-4.35270.23861420.22163470X-RAY DIFFRACTION83
4.3527-4.78910.25511430.20693488X-RAY DIFFRACTION84
4.7891-5.47830.25731470.22483544X-RAY DIFFRACTION84
5.4783-6.88770.27571430.24393511X-RAY DIFFRACTION84
6.8877-29.62590.26431440.2333474X-RAY DIFFRACTION81

+
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