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Yorodumi- PDB-1ru3: Crystal Structure of the monomeric acetyl-CoA synthase from Carbo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ru3 | ||||||
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Title | Crystal Structure of the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans | ||||||
Components | Acetyl-CoA synthase | ||||||
Keywords | OXIDOREDUCTASE / Nickel / Cluster A | ||||||
Function / homology | Function and homology information CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Carboxydothermus hydrogenoformans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Svetlitchnyi, V. / Dobbek, H. / Meyer-Klaucke, W. / Meins, T. / Thiele, B. / Rmer, P. / Huber, R. / Meyer, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans Authors: Svetlitchnyi, V. / Dobbek, H. / Meyer-Klaucke, W. / Meins, T. / Thiele, B. / Rmer, P. / Huber, R. / Meyer, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ru3.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ru3.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ru3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ru3_validation.pdf.gz | 463.4 KB | Display | wwPDB validaton report |
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Full document | 1ru3_full_validation.pdf.gz | 526.5 KB | Display | |
Data in XML | 1ru3_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 1ru3_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/1ru3 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/1ru3 | 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
#1: Protein | Mass: 82313.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Carboxydothermus hydrogenoformans (bacteria) References: UniProt: P83789 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SF4 / | #4: Chemical | ChemComp-GOL / #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: 3.97 Å3/Da / Density % sol: 69.03 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: ammonium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 2 mM / Common name: sodium-dithionite / Details: pH6.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.733, 1.7421, 1.47, 1.05 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2002 | |||||||||||||||
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→20 Å / Num. obs: 64871 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 97.2 | |||||||||||||||
Reflection | *PLUS % possible obs: 97.6 % / Num. measured all: 301338 / Rmerge(I) obs: 0.049 | |||||||||||||||
Reflection shell | *PLUS Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å |