[English] 日本語
Yorodumi
- PDB-1tff: Structure of Otubain-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tff
TitleStructure of Otubain-2
ComponentsUbiquitin thiolesterase protein OTUB2
KeywordsHYDROLASE
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
Ubiquitin thioesterase OTUB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsNanao, M.H. / Tcherniuk, S.O. / Chroboczek, J. / Dideberg, O. / Dessen, A. / Balakirev, M.Y.
CitationJournal: Embo Rep. / Year: 2004
Title: Crystal structure of human otubain 2.
Authors: Nanao, M.H. / Tcherniuk, S.O. / Chroboczek, J. / Dideberg, O. / Dessen, A. / Balakirev, M.Y.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin thiolesterase protein OTUB2


Theoretical massNumber of molelcules
Total (without water)27,4451
Polymers27,4451
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.433, 65.401, 76.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 27444.861 Da / Num. of mol.: 1 / Fragment: Otubain-2 / Mutation: G49R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB2, OTB2, OTU2, C14ORF137 / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: HYDROLASE
References: UniProt: Q96DC9, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 4000, 0.1 M HEPES, pH 7.0, 12 % isopropanol and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 288.15K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11051
21051
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.97630, 0.97990, 0.98010
SYNCHROTRONESRF ID14-420.9795
Detector
TypeIDDetector
MARRESEARCH1CCD
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97991
30.98011
40.97951
ReflectionResolution: 2.1→100 Å / Num. all: 14128 / Num. obs: 14128 / % possible obs: 99.7 % / Redundancy: 27 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.11
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.273 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→49.39 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 4.348 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25689 700 5 %RANDOM
Rwork0.18792 ---
all0.19125 ---
obs0.19125 13320 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.82 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 100 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211859
X-RAY DIFFRACTIONr_bond_other_d0.0020.021664
X-RAY DIFFRACTIONr_angle_refined_deg2.3821.9412505
X-RAY DIFFRACTIONr_angle_other_deg1.0633864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7075219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.150.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022055
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02415
X-RAY DIFFRACTIONr_nbd_refined0.2330.2428
X-RAY DIFFRACTIONr_nbd_other0.2530.21921
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.21155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7921.51102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.07621779
X-RAY DIFFRACTIONr_scbond_it4.3413757
X-RAY DIFFRACTIONr_scangle_it6.5214.5726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 57
Rwork0.158 864

+
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