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- PDB-1ziy: Crystal Structure Analysis of the dienelactone hydrolase mutant (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ziy | ||||||
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Title | Crystal Structure Analysis of the dienelactone hydrolase mutant (C123S) bound with the PMS moiety of the protease inhibitor, Phenylmethylsulfonyl fluoride (PMSF)- 1.9 A | ||||||
![]() | Carboxymethylenebutenolidase | ||||||
![]() | HYDROLASE / alpha and beta proteins / 3-D structure / Serine esterase / Aromatic hydrocarbons catabolism / PMSF | ||||||
Function / homology | ![]() carboxymethylenebutenolidase / carboxymethylenebutenolidase activity / : Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kim, H.-K. / Liu, J.-W. / Carr, P.D. / Ollis, D.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.1 KB | Display | ![]() |
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Full document | ![]() | 444.1 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zi6C ![]() 1zi8C ![]() 1zi9C ![]() 1zicC ![]() 1zixC ![]() 1zj4C ![]() 1zj5C ![]() 1dinS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25649.934 Da / Num. of mol.: 1 / Mutation: C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.84 % / 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: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 31, 2003 / Details: confocal mirrors |
Radiation | Monochromator: Osmic MaxxFlux 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: 1.9→25 Å / Num. all: 40620 / Num. obs: 39770 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.9→2.02 Å / Rmerge(I) obs: 0.149 / Num. unique all: 3398 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DIN Resolution: 1.9→20.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1183956.23 / 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: 17.8609 Å2 / ksol: 0.394774 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20.87 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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