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Yorodumi- PDB-1dm3: ACETYLATED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dm3 | ||||||
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Title | ACETYLATED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH ACETYL-COA | ||||||
Components | BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89 | ||||||
Keywords | TRANSFERASE / BIOSYNTHETIC THIOLASE / REACTION INTERMEDIATE / ACETYL-COA / BETA-ALPHA FOLD / ACETYL-COA ACETYLTRANSFERASE | ||||||
Function / homology | Function and homology information poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Zoogloea ramigera (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Modis, Y. / Wierenga, R.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystallographic analysis of the reaction pathway of Zoogloea ramigera biosynthetic thiolase. Authors: Modis, Y. / Wierenga, R.K. #1: Journal: Structure / Year: 1999 Title: A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism Authors: Modis, Y. / Wierenga, R.K. #2: Journal: Biochemistry / Year: 1989 Title: Mechanistic studies on beta-ketoacyl thiolase from Zoogloea ramigera: identification of the active-site nucleophile as Cys89, its mutation to Ser89, and kinetic and thermodynamic ...Title: Mechanistic studies on beta-ketoacyl thiolase from Zoogloea ramigera: identification of the active-site nucleophile as Cys89, its mutation to Ser89, and kinetic and thermodynamic characterization of wild-type and mutant enzymes Authors: Thompson, S. / Mayerl, F. / Peoples, O.P. / Masamune, S. / Sinskey, A.J. / Walsh, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dm3.cif.gz | 306.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dm3.ent.gz | 255.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm3 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm3 | HTTPS FTP |
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-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: 40297.949 Da / Num. of mol.: 4 / Fragment: ENTIRE THIOLASE, ACETYLATED AT CYS89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zoogloea ramigera (bacteria) / Cellular location: CYTOPLASM / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACO / #4: 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: 3.08 Å3/Da / Density % sol: 60.11 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.9 M Ammonium sulfate, 1 M lithium sulfate, 0,1 M sodium acetate, 1 mM DTT, 1mM EDTA, 1mM sodium azide, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 1.057486 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.057486 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 132107 / Num. obs: 126823 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.03→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Num. unique all: 16710 / % possible all: 94.5 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 96 % |
Reflection shell | *PLUS % possible obs: 94.5 % / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Resolution: 2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Weighted sparse matrix least squares procedure
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.214 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |