+Open data
-Basic information
Entry | Database: PDB / ID: 1ju3 | ||||||
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Title | BACTERIAL COCAINE ESTERASE COMPLEX WITH TRANSITION STATE ANALOG | ||||||
Components | cocaine esterase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase | ||||||
Function / homology | Function and homology information cocaine esterase / cocaine catabolic process / carboxylic ester hydrolase activity / dipeptidyl-peptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodococcus sp. MB1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Larsen, N.A. / Turner, J.M. / Stevens, J. / Rosser, S.J. / Basran, A. / Lerner, R.A. / Bruce, N.C. / Wilson, I.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Crystal structure of a bacterial cocaine esterase. Authors: Larsen, N.A. / Turner, J.M. / Stevens, J. / Rosser, S.J. / Basran, A. / Lerner, R.A. / Bruce, N.C. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ju3.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ju3.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ju3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ju3_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 1ju3_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 1ju3_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 1ju3_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1ju3 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1ju3 | HTTPS FTP |
-Related structure data
Related structure data | 1ju4SC 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: 63351.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. MB1 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L9D7 |
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#2: Chemical | ChemComp-PBC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10mM DTT, 10mM Tris pH 7.5, 25 mM NaCl, 1.6 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 22.5K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.58→20 Å / Num. all: 90349 / Num. obs: 90349 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064 | |||||||||||||||
Reflection shell | Resolution: 1.58→1.61 Å / Rmerge(I) obs: 0.514 / % possible all: 71.2 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 5.4 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 71.2 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JU4, cocE enzyme Resolution: 1.58→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.1881 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.1312 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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