[English] 日本語
Yorodumi- PDB-3wkl: The periplasmic PDZ tandem fragment of the RseP homologue from Aq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wkl | ||||||
---|---|---|---|---|---|---|---|
Title | The periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus | ||||||
Components | Putative Zinc Metalloprotease AQ_1964 | ||||||
Keywords | HYDROLASE / PDZ DOMAIN | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Nogi, T. / Tabata, S. / Tamura-kawakami, K. / Takagi, J. | ||||||
Citation | Journal: Structure / Year: 2013 Title: A Structure-Based Model of Substrate Discrimination by a Noncanonical PDZ Tandem in the Intramembrane-Cleaving Protease RseP Authors: Hizukuri, Y. / Oda, T. / Tabata, S. / Tamura-kawakami, K. / Oi, R. / Sato, M. / Takagi, J. / Akiyama, Y. / Nogi, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wkl.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wkl.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wkl_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wkl_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 3wkl_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3wkl_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkl ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkl | HTTPS FTP |
-Related structure data
Related structure data | 3wkmC 2zplS 2zpmS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19997.455 Da / Num. of mol.: 1 / Fragment: PDZ TANDEM FRAGMENT, UNP RESIDUES 115-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Strain: VF5 / Gene: AQ_1964 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O67776, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.75 Å3/Da / Density % sol: 74.13 % |
---|---|
Crystal grow | pH: 4.5 Details: 1.5M AMMONIUM SULFATE, 0.1M SODIUM ACCETATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 21, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.1 Å / Num. obs: 10257 / % possible obs: 99.8 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZPL, 2ZPM Resolution: 2.8→39.44 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.077 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|