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- PDB-1orb: ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF ... -

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Basic information

Entry
Database: PDB / ID: 1orb
TitleACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF RHODANESE
ComponentsCARBOXYMETHYLATED RHODANESE
KeywordsSULFURTRANSFERASE / THIOSULFATE:CYANIDE SULFURTRANSFERASE
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
ACETATE ION / Thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 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: 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: 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.J. / Heinrikson, W.G.J. / Keim, R.L. / Weng, P.S. / Russel, J.
History
DepositionJul 24, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYMETHYLATED RHODANESE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2682
Polymers33,2091
Non-polymers591
Water1,820101
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 CARBOXYMETHYLATED RHODANESE


Mass: 33208.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00586, thiosulfate sulfurtransferase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE: CARBOXYMETHYLATED RHODANESE. CARBOXYMETHYLATED AT CYS 247.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.92 %
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 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 2 % / Rmerge(I) obs: 0.097
Reflection
*PLUS
Num. obs: 13451 / % possible obs: 61 % / Num. measured all: 25157 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
TNTrefinement
SAINTdata reduction
RefinementResolution: 2→9 Å / σ(F): 0 /
RfactorNum. reflection
obs0.187 13451
Refinement stepCycle: LAST / Resolution: 2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 0 102 2432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg3.1
X-RAY DIFFRACTIONt_dihedral_angle_d19.1
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.007
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.02
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.1

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