+Open data
-Basic information
Entry | Database: PDB / ID: 3ium | ||||||
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Title | apPEP_WTX 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 / MOLECULAR REPLACEMENT / Resolution: 2.25 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 | 3ium.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ium.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ium.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/3ium ftp://data.pdbj.org/pub/pdb/validation_reports/iu/3ium | HTTPS FTP |
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-Related structure data
Related structure data | 3iujSC 3iulC 3iunC 3iuqC 3iurC 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: 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 | ||||
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#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 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % |
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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 |
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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: 2.25→40 Å / Num. all: 48135 / Num. obs: 47607 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 42.1 Å2 / Rsym value: 0.068 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.438 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3IUJ Resolution: 2.25→38.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1705237.7 / 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: 71.9455 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→38.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.33 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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