[English] 日本語
Yorodumi
- PDB-2ora: RHODANESE (THIOSULFATE: CYANIDE SULFURTRANSFERASE) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ora
TitleRHODANESE (THIOSULFATE: CYANIDE SULFURTRANSFERASE)
ComponentsOXIDIZED RHODANESE
KeywordsTRANSFERASE / MITOCHONDRION
Function / homology
Function and homology information


rRNA transport / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / rRNA import into mitochondrion / 5S rRNA binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.99 Å
AuthorsGliubich, F. / Gazerro, M. / Zanotti, G. / Delbono, S. / Berni, R.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Active site structural features for chemically modified forms of rhodanese.
Authors: Gliubich, F. / Gazerro, M. / Zanotti, G. / Delbono, S. / Bombieri, G. / Berni, R.
#1: Journal: Fundam.Appl.Toxicol. / Year: 1983
Title: The High Resolution Three-Dimensional Structure of Bovine Liver Rhodanese
Authors: Hol, W.G.J. / Lijk, L.J. / Kalk, K.H.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: The Structure of Bovine Liver Rhodanese. II. The Active Site in the Sulfur-Substituted and the Sulfur-Free Enzyme
Authors: Ploegman, J.H. / Drent, G. / Kalk, K.H. / Hol, W.G.
#3: Journal: Nature / Year: 1978
Title: The Covalent and Tertiary Structure of Bovine Liver Rhodanese
Authors: Ploegman, J.H. / Drent, G. / Kalk, K.H. / Hol, W.G. / Heinrikson, R.L. / Keim, P. / Weng, L. / Russell, J.
History
DepositionFeb 22, 1996Processing site: BNL
SupersessionAug 1, 1996ID: 1ORA
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OXIDIZED RHODANESE


Theoretical massNumber of molelcules
Total (without water)33,2251
Polymers33,2251
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.230, 49.040, 42.250
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein OXIDIZED RHODANESE


Mass: 33224.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00586, thiosulfate sulfurtransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8-1.9 Mammonium salfate1reservoir
230 mMsodium phosphate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 19026 / % possible obs: 85.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Num. measured all: 46251

-
Processing

Software
NameClassification
TNTrefinement
SAINTdata reduction
RefinementResolution: 1.99→9 Å / Num. reflection obs: 19026 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 1.99→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 81 2407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_dihedral_angle_d18
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.006
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.04
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 9 Å / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18
X-RAY DIFFRACTIONt_plane_restr0.006

+
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