+Open data
-Basic information
Entry | Database: PDB / ID: 1ec9 | ||||||
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Title | E. COLI GLUCARATE DEHYDRATASE BOUND TO XYLAROHYDROXAMATE | ||||||
Components | GLUCARATE DEHYDRATASE | ||||||
Keywords | LYASE / Glucarate Dehydratase Enolase Enzyme Superfamily TIM Barrel (beta/alpha)7beta barrel | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Evolution of 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. #1: Journal: Biochemistry / Year: 1998 Title: Evolution of Enzymative Activities in the Enolase Superfamily: Crystal Structure of (D)-glucarate Dehydratase from Pseudomonas putida Authors: Gulick, A.M. / Palmer, D.R. / Babbitt, P.C. / 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 | 1ec9.cif.gz | 371.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ec9.ent.gz | 298.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ec9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ec9_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 1ec9_full_validation.pdf.gz | 536.5 KB | Display | |
Data in XML | 1ec9_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 1ec9_validation.cif.gz | 113.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/1ec9 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/1ec9 | HTTPS FTP |
-Related 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: 49196.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET / Production host: Escherichia coli (E. coli) References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-XYH / #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: 2.68 Å3/Da / Density % sol: 54.03 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 8 Details: 1:1 mixture of protein and 14 % PEG5000 Monomethylether 75 mM MgCl2 5 % isopropanol 50 mM Hepps , pH 8.0, Microbatch, temperature 4.0K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: used microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1201 |
Detector | Type: OTHER / Detector: CCD / Date: Jul 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1201 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 516114 / Num. obs: 515842 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.189 / Num. unique all: 12784 / % possible all: 93.5 |
Reflection | *PLUS Num. obs: 133202 / Num. measured all: 516114 |
Reflection shell | *PLUS % possible obs: 93.5 % |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 0 / Rfactor all: 0.179 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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