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Yorodumi- PDB-1zj4: Crystal Structure Analysis of the dienelactone hydrolase mutant (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zj4 | ||||||
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Title | Crystal Structure Analysis of the dienelactone hydrolase mutant (E36D, C123S) bound with the PMS moiety of the protease inhibitor, Phenylmethylsulfonyl fluoride (PMSF)- 1.7 A | ||||||
Components | Carboxymethylenebutenolidase | ||||||
Keywords | HYDROLASE / alpha and beta proteins / 3-D structure / Serine esterase / Aromatic hydrocarbons catabolism / PMSF | ||||||
Function / homology | Function and homology information carboxymethylenebutenolidase / carboxymethylenebutenolidase activity / catabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 1zj4.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zj4.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zj4_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 1zj4_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 1zj4_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1zj4_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/1zj4 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/1zj4 | HTTPS FTP |
-Related structure data
Related structure data | 1zi6C 1zi8C 1zi9C 1zicC 1zixC 1ziyC 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: 25635.908 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 | #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: 2.42 Å3/Da / Density % sol: 48.71 % / 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 17, 2002 / Details: confocal mirrors |
Radiation | Monochromator: Osmic MaxFlux Confocal optics (green) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 55360 / Num. obs: 55328 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.81 Å / Rmerge(I) obs: 0.212 / Num. unique all: 4831 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DIN Resolution: 1.7→19.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1016772.8 / 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: 17.3173 Å2 / ksol: 0.395265 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.71 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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