+Open data
-Basic information
Entry | Database: PDB / ID: 1jct | ||||||
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Title | Glucarate Dehydratase, N341L mutant Orthorhombic Form | ||||||
Components | Glucarate Dehydratase | ||||||
Keywords | LYASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 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: Evolution of Enzymatic Active Sites 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 | 1jct.cif.gz | 179.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jct.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jct_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 1jct_full_validation.pdf.gz | 496.4 KB | Display | |
Data in XML | 1jct_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 1jct_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jct ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jct | HTTPS FTP |
-Related structure data
Related structure data | 1jdfC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49195.910 Da / Num. of mol.: 2 / Mutation: N341L 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): BL21(DE3) References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.6 Å3/Da / Density % sol: 52.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Peg5000 monomethylether, 50 mM MgCl, 5% isopropanol, 50 mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method / 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-BM |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 23, 2000 |
Radiation | Monochromator: 0.1 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. all: 27057 / Num. obs: 24649 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.394 / % possible all: 93.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 100153 |
Reflection shell | *PLUS % possible obs: 93.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EC8 Resolution: 2.75→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 55 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.03
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.213 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 55 Å2 | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.449 / Rfactor Rwork: 0.347 |