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- PDB-2y50: Crystal Structure of Collagenase G from Clostridium histolyticum ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y50 | ||||||
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Title | Crystal Structure of Collagenase G from Clostridium histolyticum at 2. 80 Angstrom Resolution | ||||||
![]() | COLLAGENASE | ||||||
![]() | HYDROLASE / GLUZINCIN / METALLOPROTEASE | ||||||
Function / homology | ![]() tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eckhard, U. / Brandstetter, H. | ||||||
![]() | ![]() Title: Structure of Collagenase G Reveals a Chew-and -Digest Mechanism of Bacterial Collagenolysis Authors: Eckhard, U. / Schoenauer, E. / Nuess, D. / Brandstetter, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.7 KB | Display | ![]() |
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PDB format | ![]() | 236.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2y3uSC ![]() 2y6iC ![]() 2y72C S: Starting model for refinement C: citing same article ( |
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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: 89031.945 Da / Num. of mol.: 1 / Fragment: RESIDUES 119-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-P6G / |
#4: Chemical | ChemComp-FLC / |
#5: Water | ChemComp-HOH / |
Sequence details | SEQUENCE VARIATIONS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 8.3 / Details: 23% PEG3350, 0.12M TRISODIUM CITRATE PH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2007 / Details: TORODIAL FOCUSING MIRROR |
Radiation | Monochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35.56 Å / Num. obs: 28517 / % possible obs: 98.9 % / Observed criterion σ(I): 2.8 / Redundancy: 6.9 % / Biso Wilson estimate: 72.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.8 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y3U Resolution: 2.8→34.83 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 41.423 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. CATALYTIC ZN BINDING SITE IS FORMED BY HIS523, HIS527 AND GLU555
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→34.83 Å
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Refine LS restraints |
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