+Open data
-Basic information
Entry | Database: PDB / ID: 1jdf | ||||||
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Title | Glucarate Dehydratase from E.coli N341D mutant | ||||||
Components | Glucarate Dehydratase | ||||||
Keywords | LYASE / TIM Barrel / alpha/beta barrel / Enolase Superfamily | ||||||
Function / homology | Function and homology information glucarate dehydratase activity / D-glucarate catabolic process / glucarate dehydratase / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli. Authors: Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I. #1: Journal: Biochemistry / Year: 2000 Title: Enzymatic Activities in the Enolase Superfamily: Crystallographic and Mutagenesis Studies of the Reaction Catalyzed by D-Glucarate Dehydratase from Escherichia Coli Authors: Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jdf.cif.gz | 367.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdf.ent.gz | 295.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jdf_validation.pdf.gz | 486.9 KB | Display | wwPDB validaton report |
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Full document | 1jdf_full_validation.pdf.gz | 506.4 KB | Display | |
Data in XML | 1jdf_validation.xml.gz | 74.3 KB | Display | |
Data in CIF | 1jdf_validation.cif.gz | 105.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdf ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdf | HTTPS FTP |
-Related structure data
Related structure data | 1jctC 1ec8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49197.840 Da / Num. of mol.: 4 / Mutation: N341D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GLR / #4: Chemical | ChemComp-IPA / #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: 2.61 Å3/Da / Density % sol: 52.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 8 Details: 14 % MePEG 5000, 50 mM MgCl2, 5 % 2-propanol, 50 mM HEPPS, pH 8.0, microbatch, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysis / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 136857 / Num. obs: 132888 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 505535 |
Reflection shell | *PLUS % possible obs: 89 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1EC8 Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Displacement parameters | Biso mean: 21.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.8 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.333 / Rfactor Rwork: 0.306 |