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Open data
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Basic information
Entry | Database: PDB / ID: 1amj | ||||||
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Title | STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM | ||||||
![]() | ACONITASE | ||||||
![]() | LYASE(CARBON-OXYGEN) | ||||||
Function / homology | ![]() 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 ...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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Stout, C.D. | ||||||
![]() | ![]() Title: Steric and conformational features of the aconitase mechanism. Authors: Lauble, H. / Stout, C.D. #1: ![]() Title: Crystal Structures of Aconitase with Trans-Aconitate and Nitrocitrate Bound Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D. #2: ![]() Title: Crystal Structures of Aconitase with Isocitrate and Nitroisocitrate Bound Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D. #3: ![]() Title: Structure of Activated Aconitase. Formation of the (4Fe-4S) Cluster in the Crystal Authors: Robbins, A.H. / Stout, C.D. #4: ![]() Title: The Structure of Aconitase Authors: Robbins, A.H. / Stout, C.D. #5: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.5 KB | Display | ![]() |
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PDB format | ![]() | 128.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.6 KB | Display | ![]() |
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Full document | ![]() | 421.6 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 |
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Components
#1: Protein | Mass: 82764.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-OH / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-SF4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.23 % | |||||||||||||||||||||||||
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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: 213254 / % possible obs: 92.4 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 58806 / Num. measured all: 213254 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 43.4 % / Mean I/σ(I) obs: 2.8 |
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Processing
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Refinement | Resolution: 2→8 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 57828 / Rfactor all: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.01 |