+Open data
-Basic information
Entry | Database: PDB / ID: 3iur | ||||||
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Title | apPEP_D266Nx+H2H3 opened state | ||||||
Components |
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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 / MOLECULAR REPLACEMENT / Resolution: 2.05 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iur.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iur.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 3iur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/3iur ftp://data.pdbj.org/pub/pdb/validation_reports/iu/3iur | HTTPS FTP |
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-Related structure data
Related structure data | 3iujSC 3iulC 3iumC 3iunC 3iuqC 3ivmC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 77027.492 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 | ||||||||
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#2: Protein/peptide | Mass: 2879.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized peptide #3: Chemical | #4: Chemical | ChemComp-15P / | #5: 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 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion / pH: 7.5 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), 17% w/v PEG10K) 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), 17% w/v PEG10K) were equilibrated by vapor diffusion at 14C. Crystals were soaked with the peptide H2H3. Cryosolution is precipitant plus 5% more PEG10K and 20% w/v glycerol., VAPOR DIFFUSION, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å |
Detector | Detector: CCD / Date: Jul 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. all: 64027 / Num. obs: 63835 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.084 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.05→2.12 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.441 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3IUJ Resolution: 2.05→38.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2230222.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.6271 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→38.14 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.12 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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