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Yorodumi- PDB-8acn: CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8acn | |||||||||
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Title | CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND | |||||||||
Components | ACONITASE | |||||||||
Keywords | LYASE(CARBON-OXYGEN) | |||||||||
Function / homology | Function and homology information Citric acid cycle (TCA cycle) / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / 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 | Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D. | |||||||||
Citation | 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. #1: 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. #2: Journal: Proteins / Year: 1989 Title: The Structure of Aconitase Authors: Robbins, A.H. / Stout, C.D. #3: 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 | 8acn.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8acn.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 8acn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/8acn ftp://data.pdbj.org/pub/pdb/validation_reports/ac/8acn | 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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Atom site foot note | 1: RESIDUE 325 IS A CIS PROLINE. / 2: SEE REMARK 5. |
-Components
#1: Protein | Mass: 82747.906 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-NIC / |
#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: 57.24 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion / Details: referred to J.Biol.Chem. 257.9061-9063 1982 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.05 Å / Num. all: 58710 / Num. obs: 50902 / % possible obs: 86.7 % / Num. measured all: 268600 / Rmerge(I) obs: 0.0511 |
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Reflection shell | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 2.18 Å / % possible obs: 49.8 % |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.161 / Rfactor obs: 0.161 / Highest resolution: 2 Å Details: RESIDUE 647 IS ARG FROM THE DNA SEQUENCE, (H. ZALKIN, PRIVATE COMMUNICATION) BUT CANNOT BE ACCOMMODATED AS SUCH IN THE STRUCTURE. IT HAS BEEN MODELED AS SER, BASED ON THE EXTENT OF THE SIDE CHAIN DENSITY. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.161 / Highest resolution: 2.1 Å / Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.03 |