+Open data
-Basic information
Entry | Database: PDB / ID: 4a7y | ||||||
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Title | Active site metal depleted aldos-2-ulose dehydratase | ||||||
Components | ALDOS-2-ULOSE DEHYDRATASE | ||||||
Keywords | LYASE / DEHYDRATASE/ISOMERASE / LIGNIN DEGRADATION / CORTALCERONE/MICROTHECIN FORMING / METALLOENZYME | ||||||
Function / homology | Function and homology information aldos-2-ulose dehydratase / aldos-2-ulose dehydratase activity / 1,5-anhydro-D-fructose dehydratase activity / hydro-lyase activity / metabolic process / isomerase activity / metal ion binding Similarity search - Function | ||||||
Biological species | PHANEROCHAETE CHRYSOSPORIUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Claesson, M. / Lindqvist, Y. / Madrid, S. / Sandalova, T. / Fiskesund, R. / Yu, S. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Crystal Structure of Bifunctional Aldos-2-Ulose Dehydratase/Isomerase from Phanerochaete Chrysosporium with the Reaction Intermediate Ascopyrone M. Authors: Claesson, M. / Lindqvist, Y. / Madrid, S. / Sandalova, T. / Fiskesund, R. / Yu, S. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a7y.cif.gz | 349.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a7y.ent.gz | 285.7 KB | Display | PDB format |
PDBx/mmJSON format | 4a7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a7y_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 4a7y_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 4a7y_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4a7y_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/4a7y ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a7y | HTTPS FTP |
-Related structure data
Related structure data | 4a7kSC 4a7zC C: citing same article (ref.) S: Starting model for refinement |
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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: 98852.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PHANEROCHAETE CHRYSOSPORIUM (fungus) / Production host: OGATAEA ANGUSTA (fungus) / Strain (production host): RB11(URA-) / References: UniProt: P84193, aldos-2-ulose dehydratase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Sugar | #5: 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: 2.69 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M BISTRIS-PROPANE BUFFER, PH 7, 0.2 M NACL, 10% PEG6000. THE CRYSTALS WERE SOAKED IN 10MM ANHYDROFRUCTOSE BEFORE DATA COLLECTION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.28 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→70 Å / Num. obs: 23405 / % possible obs: 88.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A7K Resolution: 2.8→56.81 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.867 / SU B: 33.643 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 36.699 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→56.81 Å
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