+Open data
-Basic information
Entry | Database: PDB / ID: 1c97 | |||||||||
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Title | S642A:ISOCITRATE COMPLEX OF ACONITASE | |||||||||
Components | MITOCHONDRIAL ACONITASE | |||||||||
Keywords | LYASE / TRICARBOXYLIC ACID CYCLE / IRON-SULFUR / MITOCHONDRION / TRANSIT PEPTIDE / 4FE-4S | |||||||||
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 / SYNCHROTRON / Resolution: 1.98 Å | |||||||||
Authors | Lloyd, S.J. / Lauble, H. / Prasad, G.S. / Stout, C.D. | |||||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex. Authors: Lloyd, S.J. / Lauble, H. / Prasad, G.S. / 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 | 1c97.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c97.ent.gz | 133.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c97_validation.pdf.gz | 411.4 KB | Display | wwPDB validaton report |
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Full document | 1c97_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 1c97_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1c97_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c97 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c97 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 82661.945 Da / Num. of mol.: 1 / Mutation: SER642ALA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P20004, aconitate hydratase |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-O / |
#4: Chemical | ChemComp-ICT / |
#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: 2.74 Å3/Da / Density % sol: 55.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7 Details: 2.6 M AMMONIUM SULFATE 0.35 M SODIUM CHLORIDE 0.25 M BIS-TRIS, pH 7.0, VAPOR DIFFUSION, temperature 295.K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 26 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→20 Å / Num. all: 219481 / Num. obs: 219481 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.368 / % possible all: 86 |
Reflection | *PLUS Num. obs: 63472 / Num. measured all: 219481 |
Reflection shell | *PLUS % possible obs: 86 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Resolution: 1.98→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.98→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.212 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |