[English] 日本語
Yorodumi- PDB-5a0s: Apo-structure of metalloprotease Zmp1 variant E143A from Clostrid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a0s | ||||||
---|---|---|---|---|---|---|---|
Title | Apo-structure of metalloprotease Zmp1 variant E143A from Clostridium difficile | ||||||
Components | ZINC METALLOPROTEASE ZMP1 | ||||||
Keywords | HYDROLASE / METALLOPROTEASE / ZMP1 / CLOSTRIDIUM DIFFICILE / PROLINE SPECIFICITY | ||||||
Function / homology | Function and homology information Pro-Pro endopeptidase / metallopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM DIFFICILE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Schacherl, M. / Pichlo, C. / Neundorf, I. / Baumann, U. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease Zmp1 Implicated in Motility of Clostridium Difficile. Authors: Schacherl, M. / Pichlo, C. / Neundorf, I. / Baumann, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a0s.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a0s.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a0s_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5a0s_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 5a0s_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5a0s_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0s ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0s | HTTPS FTP |
-Related structure data
Related structure data | 5a0pSC 5a0rC 5a0xC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.0074, 0.0013), Vector: |
-Components
#1: Protein | Mass: 21925.646 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: WITHOUT SIGNAL PEPTIDE (MISSING AA 1-26), CLEAVED N-TERMINAL HIS-TAG WITH THROMBIN, RESULTING GSH- OVERHANG Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: Q183R7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.15 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / pH: 7 / Details: 2.1 M D/L-MALIC ACID, PH 7.0 AT 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→45.9 Å / Num. obs: 12587 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 28.18 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.74 |
Reflection shell | Resolution: 2.56→2.71 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.42 / % possible all: 91.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A0P Resolution: 2.56→45.857 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 29.16 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→45.857 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|