[English] 日本語
Yorodumi- PDB-3zuk: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zuk | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN COMPLEX WITH INHIBITOR | ||||||
Components | ENDOPEPTIDASE, PEPTIDASE FAMILY M13 | ||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / PATHOGENICITY / PHAGOSOME MATURATION | ||||||
Function / homology | Function and homology information cell wall / metalloendopeptidase activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ferraris, D.M. / Sbardella, D. / Petrera, A. / Marini, S. / Amstutz, B. / Coletta, M. / Sander, P. / Rizzi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal Structure of Mycobacterium Tuberculosis Zinc-Dependent Metalloprotease-1 (Zmp1), a Metalloprotease Involved in Pathogenicity. Authors: Ferraris, D.M. / Sbardella, D. / Petrera, A. / Marini, S. / Amstutz, B. / Coletta, M. / Sander, P. / Rizzi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zuk.cif.gz | 528.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zuk.ent.gz | 434.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zuk_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3zuk_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3zuk_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 3zuk_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/3zuk ftp://data.pdbj.org/pub/pdb/validation_reports/zu/3zuk | HTTPS FTP |
-Related structure data
Related structure data | 1dmtS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 78132.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET100D/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O53649, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
---|
-Non-polymers , 11 types, 402 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-211 / | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PGE / #7: Chemical | ChemComp-PG4 / #8: Chemical | ChemComp-ACT / #9: Chemical | ChemComp-SO4 / #10: Chemical | #11: Chemical | ChemComp-CA / | #12: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | TRIETHANOLAMINE (211): POSSIBLE CONTAMINANT OF THE PHOSPHORAMIDON PREPARATION PHOSPHORAMIDON (RDF): ...TRIETHANOL |
---|---|
Sequence details | THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.9 % / Description: NONE |
---|---|
Crystal grow | pH: 4.6 Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.99 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 48222 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 75.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DMT Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 19.929 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 1.443 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE MODEL
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.02 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|