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Yorodumi- PDB-3azq: Crystal structure of puromycin hydrolase S511A mutant complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3azq | ||||||
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Title | Crystal structure of puromycin hydrolase S511A mutant complexed with PGG | ||||||
Components |
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Keywords | HYDROLASE / POP family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces morookaensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Matoba, Y. / Sugiyama, M. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structural evidence that puromycin hydrolase is a new type of aminopeptidase with a prolyl oligopeptidase family fold Authors: Matoba, Y. / Nakayama, A. / Oda, K. / Noda, M. / Kumagai, T. / Nishimura, M. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3azq.cif.gz | 265.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3azq.ent.gz | 213.5 KB | Display | PDB format |
PDBx/mmJSON format | 3azq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/3azq ftp://data.pdbj.org/pub/pdb/validation_reports/az/3azq | HTTPS FTP |
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-Related structure data
Related structure data | 3azoSC 3azpC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 71272.773 Da / Num. of mol.: 2 / Mutation: S511A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces morookaensis (bacteria) / Strain: JCM4673 / Gene: pmh / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2HXD9 #2: Protein/peptide | Mass: 229.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: purchased #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.7M ammonium sulfate, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 7, 2007 |
Radiation | Monochromator: vertically bent cylinder mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→100 Å / Num. all: 52360 / Num. obs: 52360 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5113 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AZO Resolution: 2.7→29.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2399339.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.0099 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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