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Yorodumi- PDB-1ef9: THE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ef9 | ||||||
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Title | THE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXED WITH 2S-CARBOXYPROPYL COA | ||||||
Components | METHYLMALONYL COA DECARBOXYLASE | ||||||
Keywords | LYASE / methylmalonyl coa decarboxylase / 2S-carboxypropyl | ||||||
Function / homology | Function and homology information methyl/ethyl malonyl-CoA decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / fatty acid beta-oxidation / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Benning, M.M. / Haller, T. / Gerlt, J.A. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli. Authors: Benning, M.M. / Haller, T. / Gerlt, J.A. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ef9.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ef9.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ef9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ef9_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 1ef9_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 1ef9_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1ef9_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1ef9 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1ef9 | 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: 29206.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P52045, EC: 4.1.1.41 |
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#2: Chemical | ChemComp-2CP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG8000, 50 mM magnesium chloride, 100 mM MES, 5 mM sodium azide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 49630 / Num. obs: 49630 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.7→2.82 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.152 / Num. unique all: 5502 / % possible all: 75 |
Reflection | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.043 |
-Processing
Software |
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Refinement | Resolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 Stereochemistry target values: STANDARD TNT GEOMETRY LIBRARY
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / σ(F): 0 / Rfactor all: 0.19 / Rfactor obs: 0.19 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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