+Open data
-Basic information
Entry | Database: PDB / ID: 1pdz | ||||||
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Title | X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE | ||||||
Components | ENOLASE | ||||||
Keywords | LYASE (CARBON-OXYGEN) | ||||||
Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Homarus gammarus (European lobster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Janin, J. / Duquerroy, S. / Camus, C. / Le Bras, G. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: X-ray structure and catalytic mechanism of lobster enolase. Authors: Duquerroy, S. / Camus, C. / Janin, J. #1: Journal: To be Published Title: Phasing with Mercury at 1 Angstrom Wavelength Authors: Dumas, C. / Duquerroy, S. / Janin, J. #2: Journal: Proteins / Year: 1994 Title: Lobster Enolase Crystallized by Serendipity Authors: Duquerroy, S. / Le Bras, G. / Janin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pdz.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pdz.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pdz_validation.pdf.gz | 379.1 KB | Display | wwPDB validaton report |
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Full document | 1pdz_full_validation.pdf.gz | 389 KB | Display | |
Data in XML | 1pdz_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1pdz_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/1pdz ftp://data.pdbj.org/pub/pdb/validation_reports/pd/1pdz | 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: 47124.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homarus gammarus (European lobster) / Organ: TAIL / Tissue: TAIL MUSCLE / References: UniProt: P56252, phosphopyruvate hydratase |
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#2: Chemical | ChemComp-PGA / |
#3: Chemical | ChemComp-MN / |
#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: 2.76 Å3/Da / Density % sol: 55.42 % | |||||||||||||||
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Crystal | *PLUS Density % sol: 57 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.91 Å |
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Detector | Detector: IMAGE PLATE / Date: Feb 1, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 27950 / % possible obs: 91.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.077 |
Reflection | *PLUS Num. measured all: 97010 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 43.1 % / Rmerge(I) obs: 0.393 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 37.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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