+Open data
-Basic information
Entry | Database: PDB / ID: 1ami | ||||||
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Title | STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM | ||||||
Components | ACONITASE | ||||||
Keywords | LYASE(CARBON-OXYGEN) | ||||||
Function / homology | Function and homology information Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / Mitochondrial protein degradation / tricarboxylic acid cycle / ferrous iron binding / 4 iron, 4 sulfur cluster binding ...Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / Mitochondrial protein degradation / tricarboxylic acid cycle / ferrous iron binding / 4 iron, 4 sulfur cluster binding / iron ion binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Stout, C.D. | ||||||
Citation | Journal: Proteins / Year: 1995 Title: Steric and conformational features of the aconitase mechanism. Authors: Lauble, H. / Stout, C.D. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal Structures of Aconitase with Trans-Aconitate and Nitrocitrate Bound Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D. #2: Journal: Biochemistry / Year: 1992 Title: Crystal Structures of Aconitase with Isocitrate and Nitroisocitrate Bound Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 Title: Structure of Activated Aconitase. Formation of the (4Fe-4S) Cluster in the Crystal Authors: Robbins, A.H. / Stout, C.D. #4: Journal: Proteins / Year: 1989 Title: The Structure of Aconitase Authors: Robbins, A.H. / Stout, C.D. #5: Journal: J.Biol.Chem. / Year: 1985 Title: Iron-Sulfur Cluster in Aconitase. Crystallographic Evidence for a Three-Iron Center Authors: Robbins, A.H. / Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ami.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ami.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ami.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ami_validation.pdf.gz | 407 KB | Display | wwPDB validaton report |
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Full document | 1ami_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 1ami_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1ami_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/1ami ftp://data.pdbj.org/pub/pdb/validation_reports/am/1ami | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 325 |
-Components
#1: Protein | Mass: 82764.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P20004, aconitate hydratase |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-MIC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.32 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 410465 / % possible obs: 95.4 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 60743 / Num. measured all: 410465 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 61.7 % / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 59765 / Rfactor all: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.06 |