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- PDB-1c7o: CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c7o | ||||||
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Title | CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE-L-AMINOETHOXYVINYLGLYCINE COMPLEX | ||||||
![]() | CYSTALYSIN | ||||||
![]() | TRANSFERASE / Aminotransferase | ||||||
Function / homology | ![]() cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Krupka, H.I. / Huber, R. / Holt, S.C. / Clausen, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 645.7 KB | Display | ![]() |
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PDB format | ![]() | 535.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 132.7 KB | Display | |
Data in CIF | ![]() | 176.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-PPG / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % | |||||||||||||||||||||||||
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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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 149605 / Num. obs: 106874 / % possible obs: 92.4 % / Redundancy: 1.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.204 / Num. unique all: 9997 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 149605 |
Reflection shell | *PLUS % possible obs: 87 % |
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Processing
Software | Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→20 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Software | *PLUS Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.4 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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