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Yorodumi- PDB-1eun: STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE FROM ESCH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eun | ||||||
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Title | STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE FROM ESCHERICHIA COLI | ||||||
Components | KDPG ALDOLASE2-Dehydro-3-deoxy-phosphogluconate aldolase | ||||||
Keywords | LYASE / 2-keto-3-deoxy-6-phosphogluconate aldolase / sulfate / trimer / beta-barrel | ||||||
Function / homology | Function and homology information (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / metabolic process / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Allard, J. / Grochulski, P. / Sygusch, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution. Authors: Allard, J. / Grochulski, P. / Sygusch, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eun.cif.gz | 144 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eun.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 1eun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/1eun ftp://data.pdbj.org/pub/pdb/validation_reports/eu/1eun | HTTPS FTP |
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-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: 22304.951 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P0A955, 2-dehydro-3-deoxy-phosphogluconate aldolase #2: Chemical | ChemComp-SO4 / #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: 2.34 Å3/Da / Density % sol: 47.37 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 320 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 3350, Ammonium sulfate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 320K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9789 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 43245 / Num. obs: 39588 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.66 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.269 / % possible all: 79.4 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 39315 / % possible obs: 94.8 % / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Resolution: 2→39.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 228160.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.09 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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