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Open data
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Basic information
Entry | Database: PDB / ID: 1dp2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE | ||||||
![]() | RHODANESE | ||||||
![]() | TRANSFERASE / Rhodanese / liopate / sulfurtransferase | ||||||
Function / homology | ![]() rRNA transport / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / rRNA import into mitochondrion / 5S rRNA binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Zanotti, G. / Cianci, M. | ||||||
![]() | ![]() Title: Specific interaction of lipoate at the active site of rhodanese. Authors: Cianci, M. / Gliubich, F. / Zanotti, G. / Berni, R. #1: ![]() 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: ![]() Title: ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF RHODANESE Authors: Gliubich, F. / Berni, R. / Colapietro, M. / Barba, L. / Zanotti, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.2 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.6 KB | Display | ![]() |
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Full document | ![]() | 388.3 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32983.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-LPB / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % | |||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Resolution: 2.01→55 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Param19X.pro (XPLOR)
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Refinement step | Cycle: LAST / Resolution: 2.01→55 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.01 |