+Open data
-Basic information
Entry | Database: PDB / ID: 2czq | ||||||
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Title | A novel cutinase-like protein from Cryptococcus sp. | ||||||
Components | cutinase-like protein | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryptococcus sp. (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.05 Å | ||||||
Authors | Masaki, K. / Kamini, N.R. / Ikeda, H. / Iefuji, H. / Kondo, H. / Suzuki, M. / Tsuda, S. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure and enhanced activity of a cutinase-like enzyme from Cryptococcus sp. strain S-2 Authors: Kodama, Y. / Masaki, K. / Kondo, H. / Suzuki, M. / Tsuda, S. / Nagura, T. / Shimba, N. / Suzuki, E. / Iefuji, H. #1: Journal: Appl.Environ.Microbiol. / Year: 2005 Title: Cutinase-like enzyme from the yeast Cryptococcus sp. strain S-2 hydrolyzes polylactic acid and other biodegradable plastics Authors: Masaki, K. / Kamini, N.R. / Ikeda, H. / Iefuji, H. #2: Journal: Appl.Microbiol.Biotechnol. / Year: 2012 Title: Construction of a new recombinant protein expression system in the basidiomycetous yeast Cryptococcus sp. strain S-2 and enhancement of the production of a cutinase-like enzyme Authors: Masaki, K. / Tsuchioka, H. / Hirano, T. / Kato, M. / Ikeda, H. / Iefuji, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2czq.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2czq.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 2czq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2czq ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2czq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20930.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cryptococcus sp. (fungus) / Strain: S-2 References: UniProt: Q874E9, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.10541 Å3/Da / Density % sol: 41.579067 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.9 Details: 1.3-1.6M Sodium citrate, pH 5.9, VAPOR DIFFUSION, temperature 277K |
-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 |
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Reflection | Resolution: 1.05→23 Å / Num. all: 157936 / Num. obs: 157936 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 5.364 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.067 / Net I/σ(I): 7.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / Num. unique all: 19883 / Rsym value: 0.333 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.05→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20 /
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