+Open data
-Basic information
Entry | Database: PDB / ID: 3dd5 | ||||||
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Title | Glomerella cingulata E600-cutinase complex | ||||||
Components | Cutinase | ||||||
Keywords | HYDROLASE / catalytic triad / Secreted / Serine esterase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Glomerella cingulata (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Nyon, M.P. / Rice, D.W. / Berrisford, J.M. / Hounslow, A.M. / Moir, A.J.G. / Huang, H. / Nathan, S. / Mahadi, N.M. / Farah Diba, A.B. / Craven, C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Catalysis by Glomerella cingulata Cutinase Requires Conformational Cycling between the Active and Inactive States of Its Catalytic Triad Authors: Nyon, M.P. / Rice, D.W. / Berrisford, J.M. / Hounslow, A.M. / Moir, A.J.G. / Huang, H. / Nathan, S. / Mahadi, N.M. / Bakar, F.D.A. / Craven, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dd5.cif.gz | 254 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dd5.ent.gz | 201.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/3dd5 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/3dd5 | HTTPS FTP |
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-Related structure data
Related structure data | 3dcnSC 3deaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 21094.807 Da / Num. of mol.: 8 / Fragment: residues 31-224 Source method: isolated from a genetically manipulated source Details: Cutinase (GenBank accession no. AF444194) (amino acids 31-224) Source: (gene. exp.) Glomerella cingulata (fungus) / Plasmid details: modified pET32b / Plasmid: pET32b_CutA / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: P11373, cutinase #2: Chemical | ChemComp-DEP / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, CUTI_COLGL. | |
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-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: 48 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.1M magnesium acetate, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2006 / Details: Osmic Varimax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 47279 / Num. obs: 47279 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 40.345 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6694 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DCN Resolution: 2.6→19.8 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.828 / SU B: 13.04 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.603 / ESU R Free: 0.376
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.304 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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