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Yorodumi- PDB-1jfr: CRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT 1.9A R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jfr | ||||||
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Title | CRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT 1.9A RESOLUTION: A MODEL FOR A FAMILY OF PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES | ||||||
Components | LIPASE | ||||||
Keywords | SERINE HYDROLASE / LIPASE | ||||||
Function / homology | Function and homology information 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | Streptomyces exfoliatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.9 Å | ||||||
Authors | Wei, Y. / Derewenda, Z.S. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution. Authors: Wei, Y. / Swenson, L. / Castro, C. / Derewenda, U. / Minor, W. / Arai, H. / Aoki, J. / Inoue, K. / Servin-Gonzalez, L. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jfr.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfr.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfr ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27967.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Gene: STREPTOMYCES EXFOLIATUS / Gene (production host): STREPTOMYCES EXFOLIATUS / Production host: Escherichia coli (E. coli) / References: UniProt: Q56008 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.75 / Details: pH 7.75 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 8, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 49042 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 14.75 |
Reflection | *PLUS Num. measured all: 235302 / Rmerge(I) obs: 0.054 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→8 Å / σ(F): 0 /
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Refine analyze | Luzzati coordinate error obs: 0.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.14 / Rfactor Rwork: 0.14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |