[English] 日本語
Yorodumi- PDB-1q6z: HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q6z | ||||||
---|---|---|---|---|---|---|---|
Title | HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMIN THIAZOLONE DIPHOSPHATE | ||||||
Components | Benzoylformate decarboxylase | ||||||
Keywords | LYASE / CARBON-CARBON / DECARBOXYLASE / MANDELATE CATABOLISM / THIAMIN THIAZOLONE DIPHOSPHATE / INHIBITOR / HIGH RESOLUTION | ||||||
Function / homology | Function and homology information benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 Complexed with Thiamin Thiazolone Diphosphate 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, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. #2: Journal: Biochemistry / Year: 2003 Title: Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q6z.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q6z.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 1q6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q6z_validation.pdf.gz | 705 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1q6z_full_validation.pdf.gz | 709.4 KB | Display | |
Data in XML | 1q6z_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1q6z_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q6z ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q6z | HTTPS FTP |
-Related structure data
Related structure data | 1bfdS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 56344.715 Da / Num. of mol.: 1 / Mutation: E28A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: RF4738 / Gene: MDLC / Plasmid: pRep7 / Gene (production host): MDLC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P20906, benzoylformate decarboxylase | ||||
---|---|---|---|---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 47.89 % |
---|---|
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 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2003 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1→30 Å / Num. obs: 242762 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19 | |||||||||
Reflection shell | Resolution: 1→1.03 Å / Rmerge(I) obs: 0.336 / % possible all: 40.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BFD Resolution: 1→30 Å / Num. parameters: 41647 / Num. restraintsaints: 49689 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 3771.56 / Occupancy sum non hydrogen: 4419.85 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|