+Open data
-Basic information
Entry | Database: PDB / ID: 2c0a | ||||||
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Title | Mechanism of the Class I KDPG aldolase | ||||||
Components | KHG/KDPG ALDOLASE | ||||||
Keywords | LYASE / ALDOLASE / MULTIFUNCTIONAL ENZYME / SCHIFF BASE | ||||||
Function / homology | Function and homology information (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / 4-hydroxy-2-oxoglutarate aldolase activity / metabolic process / membrane / identical protein binding ...(4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / 4-hydroxy-2-oxoglutarate aldolase activity / metabolic process / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 Å | ||||||
Authors | Hutchins, M.J. / Fullerton, S.W.B. / Toone, E.J. / Naismith, J.H. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2006 Title: Mechanism of the Class I Kdpg Aldolase. Authors: Fullerton, S.W.B. / Griffiths, J.S. / Merkel, A.B. / Cheriyann, M. / Wymer, J. / Hutchins, M.J. / Fierke, C.A. / Toone, E.J. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c0a.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c0a.ent.gz | 218.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/2c0a ftp://data.pdbj.org/pub/pdb/validation_reports/c0/2c0a | 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: 22361.018 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P10177, UniProt: P0A955*PLUS, 4-hydroxy-2-oxoglutarate aldolase, 2-dehydro-3-deoxy-phosphogluconate aldolase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 45 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 45 TO ASN ...ENGINEERED | |
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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: 1.99 Å3/Da / Density % sol: 37.67 % |
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Crystal grow | pH: 5 / Details: pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 82974 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.55→40.16 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.05 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS ADDITIONAL DENSITY IN SOME SUBUNITS FOR A CARBINOLAMINE ATTACHED TO THE ACTIVE SITE LYSINE 133. INCLUSION IN THE MODEL DID NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS ADDITIONAL DENSITY IN SOME SUBUNITS FOR A CARBINOLAMINE ATTACHED TO THE ACTIVE SITE LYSINE 133. INCLUSION IN THE MODEL DID NOT GIVE A SATISFACTORY MAP OR MODEL AFTER REFINEMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40.16 Å
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Refine LS restraints |
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