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Yorodumi- PDB-3qke: Crystal structure of D-mannonate dehydratase from Chromohalobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qke | |||||||||
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Title | Crystal structure of D-mannonate dehydratase from Chromohalobacter Salexigens complexed with Mg and D-Gluconate | |||||||||
Components | Mandelate racemase/muconate lactonizing enzyme | |||||||||
Keywords | ISOMERASE / enolase fold / D-MANNONATE DEHYDRATASE / D-Gluconate | |||||||||
Function / homology | Function and homology information gluconate dehydratase / gluconate dehydratase activity / mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Chromohalobacter salexigens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C. | |||||||||
Citation | Journal: To be Published Title: Cystal structure of D-mannonate dehydratase from Chromohalobacter salexigens complexed with Mg and D-Gluconate Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qke.cif.gz | 672.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qke.ent.gz | 550.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/3qke ftp://data.pdbj.org/pub/pdb/validation_reports/qk/3qke | HTTPS FTP |
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-Related structure data
Related structure data | 3ow1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45468.258 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89 #2: Sugar | ChemComp-GCO / #3: Chemical | ChemComp-MG / #4: 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: 2.11 Å3/Da / Density % sol: 41.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 % PEG 3350, 0.2 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→41.217 Å / Num. all: 398136 / Num. obs: 398136 / % possible obs: 91.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3OW1 Resolution: 1.55→41.217 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 24.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.148 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.55→41.217 Å
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Refine LS restraints |
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LS refinement shell |
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