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- PDB-2ora: RHODANESE (THIOSULFATE: CYANIDE SULFURTRANSFERASE) -

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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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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