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Yorodumi- PDB-1jkm: BREFELDIN A ESTERASE, A BACTERIAL HOMOLOGUE OF HUMAN HORMONE SENS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jkm | ||||||
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Title | BREFELDIN A ESTERASE, A BACTERIAL HOMOLOGUE OF HUMAN HORMONE SENSITIVE LIPASE | ||||||
Components | BREFELDIN A ESTERASE | ||||||
Keywords | SERINE HYDROLASE / DEGRADATION OF BREFELDIN A / ALPHA/BETA HYDROLASE FAMILY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å | ||||||
Authors | Wei, Y. / Contreras, A.J. / Sheffield, P. / Osterlund, T. / Derewenda, U. / Matern, U.O. / Derewenda, Z.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase. Authors: Wei, Y. / Contreras, J.A. / Sheffield, P. / Osterlund, T. / Derewenda, U. / Kneusel, R.E. / Matern, U. / Holm, C. / 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 | 1jkm.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jkm.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jkm_validation.pdf.gz | 378 KB | Display | wwPDB validaton report |
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Full document | 1jkm_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 1jkm_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 1jkm_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/1jkm ftp://data.pdbj.org/pub/pdb/validation_reports/jk/1jkm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38563.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: GenBank: 3025874, UniProt: O68884*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging dropDetails: drop contained equal volume of protein and reservoir solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.54 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 62664 / % possible obs: 86 % / Redundancy: 1.8 % / Rsym value: 0.108 / Net I/σ(I): 9.4 |
Reflection | *PLUS % possible obs: 85.8 % / Num. measured all: 206345 / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.88 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.85→8 Å / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 18.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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