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Yorodumi- PDB-1elu: COMPLEX BETWEEN THE CYSTINE C-S LYASE C-DES AND ITS REACTION PROD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1elu | ||||||
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Title | COMPLEX BETWEEN THE CYSTINE C-S LYASE C-DES AND ITS REACTION PRODUCT CYSTEINE PERSULFIDE. | ||||||
Components | L-CYSTEINE/L-CYSTINE C-S LYASE | ||||||
Keywords | LYASE / FeS cluster biosynthesis / pyridoxal 5'-phosphate / thiocysteine / aminoacrylate / enzyme-product complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å | ||||||
Authors | Clausen, T. / Kaiser, J.T. / Steegborn, C. / Huber, R. / Kessler, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structure of the cystine C-S lyase from Synechocystis: stabilization of cysteine persulfide for FeS cluster biosynthesis. Authors: Clausen, T. / Kaiser, J.T. / Steegborn, C. / Huber, R. / Kessler, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1elu.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1elu.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 1elu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1elu_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1elu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1elu_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 1elu_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/1elu ftp://data.pdbj.org/pub/pdb/validation_reports/el/1elu | 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: 42846.578 Da / Num. of mol.: 2 Fragment: 11 RESIDUES OF THE WT-N-TERMINUS REPLACED BY OCTAPEPTIDE Mutation: MADPVNLIPDR TO MTMITPSL Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6714 / Production host: Bacteria (eubacteria) / References: UniProt: Q9ZHG9 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CSS / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.42 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG8000, ammonium sulfate, phosphate, citrate, barium chloride, cysteine, cystine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 33 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.89 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25 Å / Num. all: 224370 / Num. obs: 95716 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.55→1.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.365 / % possible all: 87.3 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 224370 |
Reflection shell | *PLUS % possible obs: 87.3 % / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Resolution: 1.55→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum-likelihood on amplitudes
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Refinement step | Cycle: LAST / Resolution: 1.55→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.214 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.4 Å2 |