+Open data
-Basic information
Entry | Database: PDB / ID: 1ef8 | ||||||
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Title | CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE | ||||||
Components | METHYLMALONYL COA DECARBOXYLASE | ||||||
Keywords | LYASE / methylmalonyl coa / decarboxylase | ||||||
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: 1.85 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 | 1ef8.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ef8.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ef8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ef8_validation.pdf.gz | 381.8 KB | Display | wwPDB validaton report |
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Full document | 1ef8_full_validation.pdf.gz | 403.8 KB | Display | |
Data in XML | 1ef8_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1ef8_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1ef8 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1ef8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29206.561 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P52045, EC: 4.1.1.41 #2: Chemical | ChemComp-NI / | #3: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54.8 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: batch / pH: 9 Details: PEG8000, 100 mM Ammonium Sulfate, 100 mM CHES, 5 mM Sodium Azide, pH 9.0, Batch, temperature 288K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: used microseeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 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: Apr 7, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 81399 / Num. obs: 72476 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.85→1.93 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.104 / Num. unique all: 7996 / % possible all: 77.2 |
Reflection | *PLUS Rmerge(I) obs: 0.0225 |
-Processing
Software |
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Refinement | Resolution: 1.85→30 Å / σ(F): 0 / σ(I): 0 Stereochemistry target values: STANDARD TNT GEOMETRY LIBRARY
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor all: 0.18 / Rfactor obs: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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