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Yorodumi- PDB-1s89: H98N Mutant of Methylglyoxal Synthase from E. coli complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s89 | ||||||
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Title | H98N 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: 2.22 Å | ||||||
Authors | Marks, G.T. / Harrison, D.H. / 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 | 1s89.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s89.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 1s89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/1s89 ftp://data.pdbj.org/pub/pdb/validation_reports/s8/1s89 | 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: 16913.500 Da / Num. of mol.: 6 / Mutation: H98N 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: 59.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 1500, Sodium Cacodylate, pH 6.2, 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: May 9, 2002 |
Radiation | Monochromator: Osmic Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→29.24 Å / Num. obs: 60966 / Observed criterion σ(F): 0 / Biso Wilson estimate: 11.6 Å2 / Limit h max: 23 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 79 / Limit l min: 0 / Observed criterion F max: 120436.53 / Observed criterion F min: 0.172 |
Reflection shell | Resolution: 2.2→2.24 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→29.24 Å / Rfactor Rfree error: 0.004 / 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: 26.6625 Å2 / ksol: 0.298543 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.18 Å2 / Biso mean: 27.32 Å2 / Biso min: 7.87 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→29.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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