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Yorodumi- PDB-1dtn: MANDELATE RACEMASE MUTANT D270N CO-CRYSTALLIZED WITH (S)-ATROLACTATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dtn | ||||||
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Title | MANDELATE RACEMASE MUTANT D270N CO-CRYSTALLIZED WITH (S)-ATROLACTATE | ||||||
Components | MANDELATE RACEMASE | ||||||
Keywords | RACEMASE / ISOMERASE / MANDELATE PATHWAY | ||||||
Function / homology | Function and homology information mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Clifton, J.G. / Petsko, G.A. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317. Authors: Mitra, B. / Kallarakal, A.T. / Kozarich, J.W. / Gerlt, J.A. / Clifton, J.G. / Petsko, G.A. / Kenyon, G.L. #1: Journal: Biochemistry / Year: 1991 Title: Mechanism of the Reaction Catalyzed by Mandelate Racemase. 2. Crystal Structure of Mandelate Racemase at 2.5-A Resolution: Identification of the Active Site and Possible Catalytic Residues Authors: Neidhart, D.J. / Howell, P.L. / Petsko, G.A. / Powers, V.M. / Li, R.S. / Kenyon, G.L. / Gerlt, J.A. #2: Journal: Nature / Year: 1990 Title: Mandelate Racemase and Muconate Lactonizing Enzyme are Mechanistically Distinct and Structurally Homologous Authors: Neidhart, D.J. / Kenyon, G.L. / Gerlt, J.A. / Petsko, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dtn.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtn.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtn ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38601.613 Da / Num. of mol.: 1 / Mutation: E317Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Description: TRC PROMOTER / Gene: MANDELATE RACEMASE / Plasmid: PKT230 / Gene (production host): MANDELATE RACEMASE / Production host: Escherichia coli (E. coli) / References: UniProt: P11444, mandelate racemase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-APG / |
#4: Water | ChemComp-HOH / |
Compound details | THIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT GLUTAMATE 317 -> GLUTAMINE CO-CRYSTALLIZED ...THIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT GLUTAMATE 317 -> GLUTAMINE CO-CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 3, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 24924 / % possible obs: 85.3 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / σ(F): 1 Details: RANGE_OF_ATOMS_OR_RESIDUES: LEU 18 - ALA 32 THE ELECTRON DENSITY FOR THE RESIDUES IN THE "FLAP" REGION (LEU 18 - ALA 32) INDICATED THAT THESE RESIDUES WERE PRESENT IN TWO DIFFERENT ...Details: RANGE_OF_ATOMS_OR_RESIDUES: LEU 18 - ALA 32 THE ELECTRON DENSITY FOR THE RESIDUES IN THE "FLAP" REGION (LEU 18 - ALA 32) INDICATED THAT THESE RESIDUES WERE PRESENT IN TWO DIFFERENT CONFORMATIONS. THE OCCUPANCIES OF THE TWO CONFORMATIONS WERE REFINED WITH X-PLOR, WHICH DID NOT KEEP THE SUMS OF THE TWO OCCUPANCIES EQUAL TO 1.0. AFTER THAT REFINEMENT, THE STRUCTURE WAS REFINED USING TNT, KEEPING THE OCCUPANCIES (FROM X-PLOR) CONSTANT. INSTEAD, THE B-FACTORS WERE REFINED.
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Displacement parameters | Biso mean: 19.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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