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Yorodumi- PDB-4okd: Crystal Structure of Chlamydomonas reinhardtii Isoamylase 1 (ISA1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4okd | |||||||||
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Title | Crystal Structure of Chlamydomonas reinhardtii Isoamylase 1 (ISA1) in complex with maltoheptaose | |||||||||
Components | Isoamylase | |||||||||
Keywords | HYDROLASE / GH13 glycoside hydrolase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Sim, L. / Palcic, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal Structure of the Chlamydomonas Starch Debranching Enzyme Isoamylase ISA1 Reveals Insights into the Mechanism of Branch Trimming and Complex Assembly. Authors: Sim, L. / Beeren, S.R. / Findinier, J. / Dauvillee, D. / Ball, S.G. / Henriksen, A. / Palcic, M.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4okd.cif.gz | 637.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4okd.ent.gz | 526.5 KB | Display | PDB format |
PDBx/mmJSON format | 4okd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4okd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4okd_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4okd_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 4okd_validation.cif.gz | 84.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/4okd ftp://data.pdbj.org/pub/pdb/validation_reports/ok/4okd | HTTPS FTP |
-Related structure data
Related structure data | 4j7rC 4jr7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 93054.656 Da / Num. of mol.: 2 / Fragment: UNP Residues 57-875 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ISA1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7X8Q2, isoamylase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | #4: Sugar | ChemComp-GLC / | #5: Water | ChemComp-HOH / | |
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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: 3.46 Å3/Da / Density % sol: 64.44 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 0.2M ammonium citrate tribasic, 14-20% PEG3350, pH 7.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 109429 / % possible obs: 93 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.81 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 2.3→2.44 Å / Rmerge(I) obs: 0.014 / Mean I/σ(I) obs: 1.37 / % possible all: 64.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JR7 Resolution: 2.4→45.95 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.544 / SU ML: 0.168 / SU R Cruickshank DPI: 0.2582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 51.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→45.95 Å
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Refine LS restraints |
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