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Yorodumi- PDB-1dqu: CRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dqu | ||||||
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Title | CRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS | ||||||
Components | ISOCITRATE LYASE | ||||||
Keywords | LYASE / BETA BARREL | ||||||
Function / homology | Function and homology information acetate catabolic process / methylisocitrate lyase / glyoxysome / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / carbon utilization / fatty acid catabolic process / glyoxylate cycle / peroxisomal matrix ...acetate catabolic process / methylisocitrate lyase / glyoxysome / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / carbon utilization / fatty acid catabolic process / glyoxylate cycle / peroxisomal matrix / tricarboxylic acid cycle / peroxisome / metal ion binding Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Britton, K.L. / Langridge, S.J. / Baker, P.J. / Weeradechapon, K. / Sedelnikova, S.E. / De Lucas, J.R. / Rice, D.W. / Turner, G. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans. Authors: Britton, K. / Langridge, S. / Baker, P.J. / Weeradechapon, K. / Sedelnikova, S.E. / De Lucas, J.R. / Rice, D.W. / Turner, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Isocitrate Lyase from Aspergillus Nidulans: Crystallization and X-ray Analysis of a Glyoxylate Cycle Enzyme. Authors: Langridge, S.J. / Baker, P.J. / De Lucas, J.R. / Sedelnikova, S.E. / Turner, G. / Rice, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqu.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqu.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dqu_validation.pdf.gz | 369.8 KB | Display | wwPDB validaton report |
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Full document | 1dqu_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 1dqu_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1dqu_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqu ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer constructed from chain A generated by 222 symmetry |
-Components
#1: Protein | Mass: 60398.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (mold) / Description: MULTICOPY INSERTION OF VECTOR INTO CHROMOSOME / Production host: Emericella nidulans (mold) / References: UniProt: P28298, isocitrate lyase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % | ||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 2000, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||
Crystal grow | *PLUS Details: Langridge, S.J., (1997) Acta Crystallogr., Sect.D, 53, 488. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 27, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 21252 / Num. obs: 21252 / % possible obs: 91.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.439 / Num. unique all: 1198 / % possible all: 71.9 |
Reflection | *PLUS Num. measured all: 62390 |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor all: 0.276 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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