+Open data
-Basic information
Entry | Database: PDB / ID: 3iul | ||||||
---|---|---|---|---|---|---|---|
Title | apPEP_WT1 opened state | ||||||
Components | Prolyl endopeptidase | ||||||
Keywords | HYDROLASE / prolyl endopeptidase | ||||||
Function / homology | Function and homology information prolyl oligopeptidase / serine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Aeromonas punctata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Chiu, T.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Induced-fit mechanism for prolyl endopeptidase Authors: Li, M. / Chen, C. / Davies, D.R. / Chiu, T.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3iul.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3iul.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 3iul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/3iul ftp://data.pdbj.org/pub/pdb/validation_reports/iu/3iul | HTTPS FTP |
---|
-Related structure data
Related structure data | 3iujC 3iumC 3iunC 3iuqC 3iurC 3ivmC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 77403.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas punctata (bacteria) / Gene: prolyl endopeptidase / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X6R4 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THESE ARE NOT MUTATIONS, BUT ERROR IN DNA SEQUENCING OF THE ORIGINAL DEPOSITED ...AUTHORS STATE THAT THESE ARE NOT MUTATIONS, BUT ERROR IN DNA SEQUENCING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.04 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion / pH: 6.5 Details: 8mg/ml protein in 20mM Hepes (pH7.5), 100mM NaCl, 5% w/v glycerol, 1mM EDTA, and 1mM DTT. Equal volume of protein and precipitant (20mM MES (pH 6.5), 12% w/v PEG20K) were equilibrated by ...Details: 8mg/ml protein in 20mM Hepes (pH7.5), 100mM NaCl, 5% w/v glycerol, 1mM EDTA, and 1mM DTT. Equal volume of protein and precipitant (20mM MES (pH 6.5), 12% w/v PEG20K) were equilibrated by vapor diffusion at 14C. Cryosolution is precipitant plus 5% more PEG20K and 20% w/v glycerol., VAPOR DIFFUSION, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97177,0.97934,0.97945 | ||||||||||||
Detector | Detector: CCD / Date: Apr 20, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.95→40 Å / Num. all: 64726 / Num. obs: 64722 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.077 / Net I/σ(I): 21.2 | ||||||||||||
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.416 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.95→39.59 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2106196.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.1457 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→39.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|