+Open data
-Basic information
Entry | Database: PDB / ID: 1b0j | ||||||||||||
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Title | CRYSTAL STRUCTURE OF ACONITASE WITH ISOCITRATE | ||||||||||||
Components | ACONITATE HYDRATASE | ||||||||||||
Keywords | LYASE / COMPLEX / TRANSIT PEPTIDE | ||||||||||||
Function / homology | Function and homology information aconitate hydratase / aconitate hydratase activity / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 1b0j.cif.gz | 165.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0j.ent.gz | 128.5 KB | Display | PDB format |
PDBx/mmJSON format | 1b0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b0j_validation.pdf.gz | 404.7 KB | Display | wwPDB validaton report |
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Full document | 1b0j_full_validation.pdf.gz | 422.5 KB | Display | |
Data in XML | 1b0j_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1b0j_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0j ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0j | HTTPS FTP |
-Related structure data
Related structure data | 1b0kC 1b0mC 1c96C 1c97C 1fghS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 82790.078 Da / Num. of mol.: 1 / Mutation: S642A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: HEART / Organelle: MITOCHONDRIA / Plasmid: PUC118 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P16276, aconitate hydratase |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-ICT / |
#4: 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: 2.94 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 26 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 29472 / Num. obs: 29472 / % possible obs: 88.1 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rsym value: 0.098 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.5→2.63 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.304 / % possible all: 79.4 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FGH Resolution: 2.5→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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