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Yorodumi- PDB-1wbh: Crystal structure of the E45N mutant from KDPG aldolase from Esch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wbh | ||||||
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Title | Crystal structure of the E45N mutant from KDPG aldolase from Escherichia coli | ||||||
Components | KHG/KDPG ALDOLASE | ||||||
Keywords | LYASE / ALDOLASE / KDPG ALDOLASE / ESCHERICHIA COLI | ||||||
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 / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / metabolic process / identical protein binding / membrane ...(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 / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / metabolic process / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Fullerton, S.W.B. / Merkel, A.B. / 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. / Cheriyan, M. / Wymer, N.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 | 1wbh.cif.gz | 266.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wbh.ent.gz | 218 KB | Display | PDB format |
PDBx/mmJSON format | 1wbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/1wbh ftp://data.pdbj.org/pub/pdb/validation_reports/wb/1wbh | HTTPS FTP |
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-Related structure data
Related structure data | 1wa3C 1wauC 2c0aC 1euaS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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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 Details: PHOSPHATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET30B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P10177, UniProt: P0A955*PLUS, 2-dehydro-3-deoxy-phosphogluconate aldolase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Compound details | 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: 2.3 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | pH: 4.6 Details: 0.075M SODIUM ACETATE, 0.1M AMMONIUM SULPHATE, 27%W/V PEG4000, pH 4.60 |
-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 CCD / Detector: CCD / Date: Mar 14, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / 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: 89181 / % possible obs: 99.4 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.55→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EUA 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.
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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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