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- PDB-1rhd: STRUCTURE OF BOVINE LIVER RHODANESE. I. STRUCTURE DETERMINATION A... -

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Entry
Database: PDB / ID: 1rhd
TitleSTRUCTURE OF BOVINE LIVER RHODANESE. I. STRUCTURE DETERMINATION AT 2.5 ANGSTROMS RESOLUTION AND A COMPARISON OF THE CONFORMATION AND SEQUENCE OF ITS TWO DOMAINS
ComponentsRHODANESE
KeywordsTRANSFERASE(THIOSULFATE / CYANIDE SULFUR)
Function / homology
Function and homology information


rRNA transport / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase / thiosulfate-cyanide 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 (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHol, W.G.J. / Ploegman, J.H. / Kalk, K.H. / Drent, G.
Citation
Journal: J.Mol.Biol. / Year: 1978
Title: Structure of bovine liver rhodanese. I. Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains.
Authors: Ploegman, J.H. / Drent, G. / Kalk, K.H. / Hol, W.G.
#1: Journal: Biochemistry / Year: 1983
Title: Binding of Metal Cyanide Complexes to Bovine Liver Rhodanese in the Crystalline State
Authors: Lijk, L.J. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J.
#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.J.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: The Double Domain Structure of Rhodanese
Authors: Bergsma, J. / Hol, W.G.J. / Jansonius, J.N. / Kalk, K.H. / Ploegman, J.H. / Smit, J.D.G.
#4: Journal: Thesis / Year: 1977
Title: The Three-Dimensional Structure of Bovine Liver Rhodanese
Authors: Ploegman, J.H.
#5: Journal: Isr.J.Chem. / Year: 1974
Title: The Structure of Rhodanese at 4 Angstroms Resolution. The Conformation of the Polypeptide Chain
Authors: Smit, J.D.G. / Ploegman, J.H. / Pierrot, M. / Kalk, K.H. / Jansonius, J.N. / Drenth, J.
#7: Journal: Biochem.Biophys.Res.Commun. / Year: 1971
Title: Crystallographic Data for Rhodanese from Bovine Liver
Authors: Drenth, J. / Smit, J.D.G.
#6: Journal: Thesis / Year: 1973
Authors: Smit, J.D.G.
History
DepositionNov 23, 1977Processing site: BNL
Revision 1.0Jan 16, 1978Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHODANESE


Theoretical massNumber of molelcules
Total (without water)32,9821
Polymers32,9821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.100, 49.000, 42.200
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 RHODANESE


Mass: 32982.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00586, thiosulfate sulfurtransferase
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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal grow
*PLUS
pH: 7.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate11
21 mMsodium thiosulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 0 2326
Refinement
*PLUS
Num. reflection obs: 10102
Solvent computation
*PLUS
Displacement parameters
*PLUS

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