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Yorodumi- PDB-1c7n: CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c7n | ||||||
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Title | CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE COFACTOR | ||||||
Components | CYSTALYSIN | ||||||
Keywords | TRANSFERASE / Aminotransferase / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Treponema denticola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Krupka, H.I. / Huber, R. / Holt, S.C. / Clausen, T. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme. Authors: Krupka, H.I. / Huber, R. / Holt, S.C. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c7n.cif.gz | 675.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c7n.ent.gz | 559.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c7n ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c7n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 46278.441 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema denticola (bacteria) / Plasmid: PLC67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56257 #2: Chemical | ChemComp-PLP / #3: 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: 2.31 Å3/Da / Density % sol: 46.67 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 4000, magnesium acetate, MES, pH 6.5, vapor diffusion/sitting drop, temperature 293.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 382434 / Num. obs: 254989 / % possible obs: 96.5 % / Redundancy: 1.5 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.255 / Num. unique all: 12280 / % possible all: 87.9 |
Reflection | *PLUS Num. measured all: 382434 |
Reflection shell | *PLUS % possible obs: 87.9 % |
-Processing
Refinement | Resolution: 1.9→25 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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