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Yorodumi- PDB-1s8a: H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s8a | ||||||
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Title | H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid | ||||||
Components | Methylglyoxal synthase | ||||||
Keywords | LYASE / GLYCOLYTIC BYPASS / METHYLGLYOXAL | ||||||
Function / homology | Function and homology information methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / protein hexamerization / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Harrison, D.H. / Marks, G.T. / Susler, M. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Mutagenic studies on histidine 98 of methylglyoxal synthase: effects on mechanism and conformational change. Authors: Marks, G.T. / Susler, M. / Harrison, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s8a.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s8a.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 1s8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/1s8a ftp://data.pdbj.org/pub/pdb/validation_reports/s8/1s8a | 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: 16927.525 Da / Num. of mol.: 6 / Mutation: H98Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MGSA, B0963, Z1314, ECS1047, SF0965, S1031 / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / Strain (production host): ML1 / References: UniProt: P0A731, methylglyoxal synthase #2: Chemical | ChemComp-PGA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 1500, Sodium Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 11, 2002 / Details: Osmic Confocal Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.65 Å / Num. all: 57342 / Observed criterion σ(F): 0 / Biso Wilson estimate: 14.1 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 58 / Limit k min: 0 / Limit l max: 80 / Limit l min: 0 / Observed criterion F max: 131602.62 / Observed criterion F min: 0.078 |
Reflection shell | Resolution: 2.2→2.24 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.65 Å / Rfactor Rfree error: 0.003 / Rfactor Rfree error details: shells / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 26.9713 Å2 / ksol: 0.29957 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.08 Å2 / Biso mean: 29.51 Å2 / Biso min: 7.94 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.65 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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