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- PDB-1dp2: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE -

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Basic information

Entry
Database: PDB / ID: 1dp2
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE
ComponentsRHODANESE
KeywordsTRANSFERASE / Rhodanese / liopate / sulfurtransferase
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
5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid / Thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsZanotti, G. / Cianci, M.
Citation
Journal: Biochim.Biophys.Acta / Year: 2000
Title: Specific interaction of lipoate at the active site of rhodanese.
Authors: Cianci, M. / Gliubich, F. / Zanotti, G. / Berni, R.
#1: 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. / Drenth, G. / Kalk, K.H. / Hol, W.G.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF RHODANESE
Authors: Gliubich, F. / Berni, R. / Colapietro, M. / Barba, L. / Zanotti, G.
History
DepositionDec 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 6, 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_site
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_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: RHODANESE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1902
Polymers32,9831
Non-polymers2061
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.36, 49.31, 41.68
Angle α, β, γ (deg.)90, 99.6, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RHODANESE


Mass: 32983.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00586, thiosulfate sulfurtransferase
#2: Chemical ChemComp-LPB / 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid


Mass: 206.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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 / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals were obtained from ammonium sulfate. After soaking with 28% PEG 6000, 40 mM phosphate buffer, pH=7, 4 mM DL-lipoate was added , VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K
Crystal grow
*PLUS
pH: 7.4 / Details: Gliubich, F., (1996), J. Biol. Chem., 271, 21054.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8-1.9 Mammonium sulfate1reservoir
230 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→55 Å / Num. all: 18241 / Num. obs: 18062 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 14
Reflection shellResolution: 2.01→2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.134 / Num. unique all: 3174 / % possible all: 68
Reflection
*PLUS
Num. obs: 18241 / Num. measured all: 42252
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
FRAMBOdata collection
SAINTdata scaling
X-PLORphasing
RefinementResolution: 2.01→55 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Param19X.pro (XPLOR)
RfactorNum. reflectionSelection details
Rfree0.23 875 random
Rwork0.17 --
all0.185 18241 -
obs0.17 18062 -
Refinement stepCycle: LAST / Resolution: 2.01→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 12 112 2451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg2.3
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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