+Open data
-Basic information
Entry | Database: PDB / ID: 1boi | ||||||
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Title | N-TERMINALLY TRUNCATED RHODANESE | ||||||
Components | RHODANESE | ||||||
Keywords | TRANSFERASE / RHODANESE / 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 | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Gliubich, F. / Berni, R. / Cianci, M. / Trevino, R.J. / Horowitz, P.M. / Zanotti, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: NH2-terminal sequence truncation decreases the stability of bovine rhodanese, minimally perturbs its crystal structure, and enhances interaction with GroEL under native conditions. Authors: Trevino, R.J. / Gliubich, F. / Berni, R. / Cianci, M. / Chirgwin, J.M. / Zanotti, G. / Horowitz, P.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of Sulfur-Substituted Rhodanese at 1.36 A Resolution Authors: Gliubich, F. / Berni, R. / Colapietro, M. / Barba, L. / Zanotti, G. #2: 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. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1boi.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1boi.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 1boi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1boi_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
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Full document | 1boi_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 1boi_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1boi_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1boi ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1boi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33240.668 Da / Num. of mol.: 1 / Fragment: DEL(1-7) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line: 293 / Cellular location: CYTOPLASM / Organ: LIVER / Plasmid: PTTQ19 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00586, thiosulfate sulfurtransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.3 / Details: pH 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55 Å / Num. obs: 109730 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / % possible all: 77.5 |
Reflection | *PLUS Num. obs: 13716 / Num. measured all: 109730 |
-Processing
Software |
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Refinement | Resolution: 2.2→55 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 0
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Refine analyze | Luzzati d res low obs: 55 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→55 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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