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Yorodumi- PDB-1po7: HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1po7 | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA | ||||||
Components | Benzoylformate decarboxylase | ||||||
Keywords | LYASE / CARBON-CARBON / DECARBOXYLASE / MANDELATE CATABOLISM / THIAMIN DIPHOSPHATE / HIGH RESOLUTION | ||||||
Function / homology | Function and homology information benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Bera, A.K. / Hasson, M.S. | ||||||
Citation | Journal: To be Published Title: High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase from Pseudomonas Putida Authors: Bera, A.K. / Anderson, N.L. / Hasson, M.S. #1: Journal: Biochemistry / Year: 1998 Title: THE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE AT 1.6 A RESOLUTION: DIVERSITY OF CATALYTIC RESIDUES IN THIAMIN DIPHOSPHATE-DEPENDENT ENZYMES Authors: HASSON, M.S. / Muscate, A. / McLeish, M.J. / POLOVNIKOVA, E.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. #2: Journal: Biochemistry / Year: 1998 Title: THE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE AT 1.6 A RESOLUTION: DIVERSITY OF CATALYTIC RESIDUES IN THIAMIN DIPHOSPHATE-DEPENDENT ENZYMES Authors: POLOVNIKOVA, E.S. / McLeish, M.J. / Sergienko, E.A. / Burgner, J.T. / Anderson, N.L. / BERA, A.K. / Jordan, F. / Kenyon, G.L. / HASSON, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1po7.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1po7.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 1po7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1po7 ftp://data.pdbj.org/pub/pdb/validation_reports/po/1po7 | HTTPS FTP |
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-Related structure data
Related structure data | 1bfdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 56344.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: MDLC / Plasmid: pRep7 / Production host: Pseudomonas putida (bacteria) / Strain (production host): RF4738 / References: UniProt: P20906, benzoylformate decarboxylase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-TZD / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2001 | |||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.2→99 Å / Num. obs: 145746 / % possible obs: 87.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.5 | |||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.247 / % possible all: 66.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BFD Resolution: 1.2→20 Å / Num. parameters: 41023 / Num. restraintsaints: 49734 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 3784.49 / Occupancy sum non hydrogen: 4425.04 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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