[English] 日本語
Yorodumi
- PDB-7pl7: Crystal structure of yeast Otu2 OTU domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pl7
TitleCrystal structure of yeast Otu2 OTU domain
ComponentsOTU domain-containing protein 2
KeywordsHYDROLASE / deubiquitination / translation / 40S ribosomal subunit
Function / homology
Function and homology information


cysteine-type deubiquitinase activity / cytoplasm
Similarity search - Function
: / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
OTU domain-containing protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIvic, N. / Cheng, J. / Becker, T. / Ikeuchi, K.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB/TRR-174 Germany
German Research Foundation (DFG)BE1814/15-1 Germany
German Research Foundation (DFG)BE1814/1-1 Germany
CitationJournal: To Be Published
Title: Crystal structure of yeast Otu2 OTU domain
Authors: Ikeuchi, K.
History
DepositionAug 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OTU domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)19,4491
Polymers19,4491
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.669, 60.055, 148.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

-
Components

#1: Protein OTU domain-containing protein 2


Mass: 19449.162 Da / Num. of mol.: 1 / Mutation: C178S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OTU2, YHL013C / Production host: Escherichia coli (E. coli) / References: UniProt: P38747
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M KSCN 0.1 M BisTris propane pH 6.5 20% PEG 3350 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 16, 2020 / Details: Si(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→42.772 Å / Num. obs: 11976 / % possible obs: 99.8 % / Redundancy: 7.091 % / Biso Wilson estimate: 62.783 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.142 / Χ2: 0.808 / Net I/σ(I): 13.95 / Num. measured all: 84923
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.59-2.757.1971.0022.3513854195419250.8981.0898.5
2.75-2.947.2320.6743.9312923178717870.9560.726100
2.94-3.176.8830.4436.5611757170817080.9770.48100
3.17-3.477.1050.27711.3411113156415640.9920.298100
3.47-3.887.3160.16617.1610162138913890.9950.179100
3.88-4.476.9380.09524.258707125512550.9970.103100
4.47-5.466.8680.07328.167301106310630.9960.08100
5.46-7.667.280.06929.3559268148140.9980.074100
7.66-42.7726.7460.04339.3231644724690.9990.04799.4

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BOU

4bou


Resolution: 2.6→42.772 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 321 4.98 %
Rwork0.2252 6124 -
obs0.2271 6445 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.99 Å2 / Biso mean: 74.6578 Å2 / Biso min: 31.24 Å2
Refinement stepCycle: final / Resolution: 2.6→42.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 27 1308
Biso mean---67.58 -
Num. residues----155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6001-3.27570.32181560.2632987
3.2757-42.7720.24781650.21443137
Refinement TLS params.Method: refined / Origin x: 10.4451 Å / Origin y: 31.7461 Å / Origin z: 56.3871 Å
111213212223313233
T0.3562 Å20.0743 Å2-0.0269 Å2-0.3425 Å2-0.0395 Å2--0.4603 Å2
L3.2086 °2-0.5789 °2-0.0527 °2-2.9988 °2-0.9976 °2--6.182 °2
S-0.1982 Å °-0.3181 Å °0.21 Å °0.2364 Å °0.1079 Å °-0.3521 Å °-0.4167 Å °0.2738 Å °0.0651 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 148 through 307)

+
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