[English] 日本語
Yorodumi
- PDB-7wuk: Crystal structure of UBR bof from PRT6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wuk
TitleCrystal structure of UBR bof from PRT6
ComponentsE3 ubiquitin-protein ligase
KeywordsLIGASE / E3 ligase UBR Box PRT6
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the N-end rule pathway / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding
Similarity search - Function
E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway
Similarity search - Domain/homology
E3 ubiquitin-protein ligase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.63 Å
AuthorsHo, M.C. / Lin, T.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of UBR box from PRT6
Authors: Ho, M.C. / Lin, T.J.
History
DepositionFeb 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1164
Polymers7,9201
Non-polymers1963
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.749, 29.749, 115.636
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein E3 ubiquitin-protein ligase / PRT6


Mass: 7919.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os01g0148000, OSNPB_010148000 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0UY23, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 8% (v/v) Tacsimate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.2831 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2831 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 14336 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.044 / Χ2: 1.254 / Net I/σ(I): 15.8 / Num. measured all: 88259
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.695.90.1314200.9920.0580.1430.675100
1.69-1.7660.10514740.9940.0460.1150.8100
1.76-1.846.20.08714150.9950.0380.0950.888100
1.84-1.936.20.07614020.9950.0330.0831.04100
1.93-2.056.20.06514280.9950.0290.0711.284100
2.05-2.216.20.05714350.9970.0250.0631.524100
2.21-2.436.20.0514580.9980.0220.0551.64100
2.43-2.796.20.0514070.9970.0220.0552.002100
2.79-3.516.20.0414450.9980.0180.0441.941100
3.51-506.30.021145210.0090.0230.70299.4

-
Phasing

Phasing
Method
SAD
molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.63→25.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.388 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 415 5.2 %RANDOM
Rwork0.1864 ---
obs0.1881 7582 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.51 Å2 / Biso mean: 15.784 Å2 / Biso min: 10.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: final / Resolution: 1.63→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms523 0 3 20 546
Biso mean--19.86 22.11 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013546
X-RAY DIFFRACTIONr_bond_other_d0.0060.018452
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.649739
X-RAY DIFFRACTIONr_angle_other_deg1.6911.5991045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.683569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14420.88234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7241581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.455155
X-RAY DIFFRACTIONr_chiral_restr0.1140.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 35 -
Rwork0.142 528 -
all-563 -
obs--100 %

+
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