+Open data
-Basic information
Entry | Database: PDB / ID: 1aco | |||||||||
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Title | CRYSTAL STRUCTURE OF ACONITASE WITH TRANSACONITATE 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 / 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 | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.05 Å | |||||||||
Authors | Stout, C.D. | |||||||||
Citation | 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. #1: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aco.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aco.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 1aco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aco_validation.pdf.gz | 404.6 KB | Display | wwPDB validaton report |
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Full document | 1aco_full_validation.pdf.gz | 420.5 KB | Display | |
Data in XML | 1aco_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 1aco_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/1aco ftp://data.pdbj.org/pub/pdb/validation_reports/ac/1aco | 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: RESIDUE 325 IS A CIS PROLINE. / 2: SEE REMARK 6. |
-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-TRA / |
#3: Chemical | ChemComp-SF4 / |
#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: seeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Num. all: 59472 / Num. obs: 54306 / % possible obs: 91.3 % / Num. measured all: 195408 / Rmerge(I) obs: 0.045 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.168 / Rfactor obs: 0.168 / Highest resolution: 2.05 Å Details: THE DENSITY FOR THE FOLLOWING REGIONS IS WEAK AND THE FINAL REBUILDING STEPS USED STEREOCHEMICAL CONSIDERATIONS - N-TERMINAL PCA ILE 433 THROUGH GLU 437 THR 488 THROUGH LYS 494 LYS 522 ...Details: THE DENSITY FOR THE FOLLOWING REGIONS IS WEAK AND THE FINAL REBUILDING STEPS USED STEREOCHEMICAL CONSIDERATIONS - N-TERMINAL PCA ILE 433 THROUGH GLU 437 THR 488 THROUGH LYS 494 LYS 522 THROUGH GLN 527 C-TERMINAL GLN 752 THROUGH LYS 754 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: 2.05 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 8 Å / Num. reflection all: 52110 / σ(F): 0 / Rfactor all: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.02 |