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Yorodumi- PDB-1poi: CRYSTAL STRUCTURE OF GLUTACONATE COENZYME A-TRANSFERASE FROM ACID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1poi | ||||||
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Title | CRYSTAL STRUCTURE OF GLUTACONATE COENZYME A-TRANSFERASE FROM ACIDAMINOCOCCUS FERMENTANS TO 2.55 ANGSTOMS RESOLUTION | ||||||
Components | (GLUTACONATE COENZYME A-TRANSFERASE) x 2 | ||||||
Keywords | TRANSFERASE / COA / GLUTAMATE / PROTEIN FERMENTATION | ||||||
Function / homology | Function and homology information glutaconate CoA-transferase / glutaconate CoA-transferase activity / glutamate catabolic process via 2-hydroxyglutarate / cytoplasm Similarity search - Function | ||||||
Biological species | Acidaminococcus fermentans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.5 Å | ||||||
Authors | Jacob, U. / Mack, M. / Clausen, T. / Huber, R. / Buckel, W. / Messerschmidt, A. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases. Authors: Jacob, U. / Mack, M. / Clausen, T. / Huber, R. / Buckel, W. / Messerschmidt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1poi.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1poi.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 1poi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1poi_validation.pdf.gz | 391 KB | Display | wwPDB validaton report |
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Full document | 1poi_full_validation.pdf.gz | 417.3 KB | Display | |
Data in XML | 1poi_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 1poi_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1poi ftp://data.pdbj.org/pub/pdb/validation_reports/po/1poi | HTTPS FTP |
-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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35390.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: Q59111 #2: Protein | Mass: 28566.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: Q59112 #3: Chemical | ChemComp-CU / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: AMMONIUM SULFATE/PEG PH=5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→7 Å / Num. obs: 37201 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.098 |
Reflection shell | Resolution: 2.55→2.64 Å / % possible all: 32 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→7 Å / Rfactor Rwork: 0.19 / Rfactor obs: 0.19 / Cross valid method: FREE-R / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 37201 / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |