+Open data
-Basic information
Entry | Database: PDB / ID: 1mzo | |||||||||
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Title | Crystal structure of pyruvate formate-lyase with pyruvate | |||||||||
Components | Pyruvate formate-lyase | |||||||||
Keywords | TRANSFERASE / ENZYME-SUBSTRATE COMPLEX | |||||||||
Function / homology | Function and homology information formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Lehtio, L. / Leppanen, V.-M. / Kozarich, J.W. / Goldman, A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of Escherichia coli pyruvate formate-lyase with pyruvate. Authors: Lehtio, L. / Leppanen, V.M. / Kozarich, J.W. / Goldman, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mzo.cif.gz | 307.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mzo.ent.gz | 250.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/1mzo ftp://data.pdbj.org/pub/pdb/validation_reports/mz/1mzo | HTTPS FTP |
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-Related structure data
Related structure data | 2pflS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 85327.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pKK223-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09373, formate C-acetyltransferase #2: Chemical | ChemComp-PGE / | #3: Chemical | #4: 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: 2.92 Å3/Da / Density % sol: 57.95 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7.3 Details: PEG1000, MOPS, ammonium chloride, na-pyruvate, DTT, magnesium chloride, EDTA, pH 7.3, MICRODIALYSIS, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9102 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 56141 / Num. obs: 55923 / % possible obs: 98.8 % / Observed criterion σ(F): -1 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 94.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 318766 / Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS % possible obs: 94.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PFL Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: 9 OF THE POLYETHYLENE GLYCOL ATOMS WERE INCLUDED IN REFINEMENT AND ATOM O1 ADDED AFTERWARDS ON SYMMETRY AXIS WITH 0.5 OCCUPANCY
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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