[English] 日本語
Yorodumi- PDB-3pk7: Crystal structure of D-mannonate dehydratase from Chromohalobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pk7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens with MG and Glycerol bound in the active site | ||||||
Components | Mandelate racemase/muconate lactonizing enzyme | ||||||
Keywords | ISOMERASE / enolase superfamily fold / MG binding | ||||||
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: 1.642 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens with MG and Glycerol bound in the active site Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pk7.cif.gz | 672.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pk7.ent.gz | 549.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/3pk7 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/3pk7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ow1S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-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: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 3350, 0.1M Succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 29, 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: 1.642→40.047 Å / Num. all: 366762 / Num. obs: 366762 / % possible obs: 99.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OW1 Resolution: 1.642→40.047 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.43 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.491 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.642→40.047 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|