[English] 日本語
Yorodumi
- PDB-5qiq: Covalent fragment group deposition -- Crystal Structure of OUTB2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qiq
TitleCovalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103050
ComponentsUbiquitin thioesterase OTUB2
Keywordshydrolase/hydrolase inhibitor / SGC - Diamond I04-1 fragment screening / XChemExplorer / PROTEASE OTUB2 / DEUBIQUITINATING ENZYME OTUB2 / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


negative regulation of double-strand break repair / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / nucleus
Similarity search - Function
Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily / Phosphorylase Kinase; domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-[(4-bromothiophen-2-yl)methyl]acetamide / DI(HYDROXYETHYL)ETHER / Ubiquitin thioesterase OTUB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.44 Å
AuthorsSethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. ...Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / London, N. / von Delft, F.
CitationJournal: To Be Published
Title: Covalent fragment group deposition
Authors: Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / London, N. / von Delft, F.
History
DepositionAug 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin thioesterase OTUB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7644
Polymers26,3621
Non-polymers4023
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.610, 58.790, 50.194
Angle α, β, γ (deg.)90.000, 116.140, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin thioesterase OTUB2 / Deubiquitinating enzyme OTUB2 / OTU domain-containing ubiquitin aldehyde-binding protein 2 / ...Deubiquitinating enzyme OTUB2 / OTU domain-containing ubiquitin aldehyde-binding protein 2 / Otubain-2 / Ubiquitin-specific-processing protease OTUB2


Mass: 26362.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB2, C14orf137, OTB2, OTU2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DC9, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-J5A / N-[(4-bromothiophen-2-yl)methyl]acetamide


Mass: 234.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8BrNOS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.39 Å3/Da / Density % sol: 48.58 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.44→45.06 Å / Num. obs: 44958 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 9.6 / Num. measured all: 149724 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.44-1.482.90.927972133200.4610.6521.1391.299.8
6.44-45.063.30.03617625300.9970.0240.04432.398.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0230refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1TFF

1tff


Resolution: 1.44→45.06 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.11 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 1983 4.4 %RANDOM
Rwork0.148 ---
obs0.1504 42954 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.78 Å2 / Biso mean: 17.878 Å2 / Biso min: 7.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.18 Å2
2--0.39 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.44→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 22 228 2075
Biso mean--27.3 31.59 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0141915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171700
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.6572587
X-RAY DIFFRACTIONr_angle_other_deg1.131.6513978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6985235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17521.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41815328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2421514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_mcbond_it3.381.49911
X-RAY DIFFRACTIONr_mcbond_other3.331.486910
X-RAY DIFFRACTIONr_mcangle_it3.9182.2441143
X-RAY DIFFRACTIONr_rigid_bond_restr3.6333615
X-RAY DIFFRACTIONr_sphericity_free27.6035157
X-RAY DIFFRACTIONr_sphericity_bonded14.71453640
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 167 -
Rwork0.273 3147 -
all-3314 -
obs--99.7 %

+
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