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Yorodumi- PDB-1zi9: Crystal Structure Analysis of the dienelactone hydrolase (E36D, C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zi9 | ||||||
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Title | Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A | ||||||
Components | Carboxymethylenebutenolidase | ||||||
Keywords | HYDROLASE / alpha and beta proteins / 3-D structure / Serine esterase / Aromatic hydrocarbons / catabolism | ||||||
Function / homology | Function and homology information carboxymethylenebutenolidase / carboxymethylenebutenolidase activity / catabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, H.-K. / Liu, J.-W. / Carr, P.D. / Ollis, D.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase. Authors: Kim, H.K. / Liu, J.W. / Carr, P.D. / Ollis, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zi9.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zi9.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zi9_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
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Full document | 1zi9_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 1zi9_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1zi9_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/1zi9 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/1zi9 | HTTPS FTP |
-Related structure data
Related structure data | 1zi6C 1zi8C 1zicC 1zixC 1ziyC 1zj4C 1zj5C 1dinS 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: 25481.721 Da / Num. of mol.: 1 / Mutation: E36D, C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: clcD / Plasmid: pCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0A114, carboxymethylenebutenolidase | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.69 % / Description: the file contains Friedel pairs. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium Citrate buffer, 1.2M Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.2915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002 / Details: confocal mirrors |
Radiation | Monochromator: Si(III) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2915 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.81 Å / Num. all: 81931 / Num. obs: 79229 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.5→1.59 Å / Rmerge(I) obs: 0.171 / Num. unique all: 7015 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DIN Resolution: 1.5→33.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1071904.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.0229 Å2 / ksol: 0.438206 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→33.81 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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