[English] 日本語
![](img/lk-miru.gif)
- PDB-2xs4: Structure of karilysin catalytic MMP domain in complex with magnesium -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2xs4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of karilysin catalytic MMP domain in complex with magnesium | ||||||
![]() |
| ||||||
![]() | HYDROLASE / BACTERIAL MMP / VIRULENCE FACTOR / METALLOPROTEASE / ZINC-DEPENDENT / PEPTIDASE | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen catabolic process / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cerda-Costa, N. / Guevara, T. / Karim, A.Y. / Ksiazek, M. / Nguyen, K.-A. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X. | ||||||
![]() | ![]() Title: The Structure of the Catalytic Domain of Tannerella Forsythia Karilysin Reveals It is a Bacterial Xenologue of Animal Matrix Metalloproteinases. Authors: Cerda-Costa, N. / Guevara, T. / Karim, A.Y. / Ksiazek, M. / Nguyen, K.A. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X. #1: Journal: Biol.Chem. / Year: 2010 Title: A Novel Matrix Metalloprotease-Like Enzyme (Karilysin) of the Periodontal Pathogen Tannerella Forsythia Atcc 43037. Authors: Karim, A.Y. / Kulczycka, M. / Kantyka, T. / Dubin, G. / Jabaiah, A. / Daugherty, P.S. / Thogersen, I.B. / Enghild, J.J. / Nguyen, K. / Potempa, J. #2: Journal: J.Innate.Immun. / Year: 2010 Title: Proteolytic Inactivation of Ll-37 by Karilysin, a Novel Virulence Mechanism of Tannerella Forsythia. Authors: Koziel, J. / Karim, A.Y. / Przybyszewska, K. / Ksiazek, M. / Rapala-Kozik, M. / Nguyen, K. / Potempa, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 89.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 66.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 433.1 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xs3SC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 18790.693 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 337.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 200 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / | ||||
---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | ZINC CATION (ZN): CATALYTIC 999 AND STRUCTURAL 998 ZINC CATIONS. MAGNESIUM CATION (MG): TENTATIVELY ...ZINC CATION (ZN): CATALYTIC 999 AND STRUCTURAL |
---|---|
Sequence details | ONLY THE CATALYTIC DOMAIN (TYR35-SER201) WAS CRYSTALLIZED. A PEPTIDE WAS FOUND AT THE ACTIVE SITE ...ONLY THE CATALYTIC DOMAIN (TYR35-SER201) WAS CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K Details: CRYSTALS OF MAGNESIUM-BOUND KLY18 WERE OBTAINED AT 4C BY MIXING PROTEIN SOLUTION PREINCUBATED WITH CALCIUM (AT 7.3MG ML-1 IN 5MM TRIS-HCL, PH8.0, 5MM CALCIUM CHLORIDE, 0.02% SODIUM AZIDE) ...Details: CRYSTALS OF MAGNESIUM-BOUND KLY18 WERE OBTAINED AT 4C BY MIXING PROTEIN SOLUTION PREINCUBATED WITH CALCIUM (AT 7.3MG ML-1 IN 5MM TRIS-HCL, PH8.0, 5MM CALCIUM CHLORIDE, 0.02% SODIUM AZIDE) AND 14% SODIUM POLYACRYLATE 5100, 20MM MAGNESIUM CHLORIDE, 0.1M HEPES, PH7.5 IN A VOLUME RATIO OF 1:3. THE LATTER CONDITIONS WERE SCALED UP TO THE MICROLITER RANGE WITH 24-WELL CRYSCHEM CRYSTALLIZATION DISHES (HAMPTON RESEARCH). |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30.3 Å / Num. obs: 21225 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.8 / % possible all: 95.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XS3 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.508 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.982 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|