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Yorodumi- PDB-2x8w: The Crystal Structure of Methylglyoxal Synthase from Thermus sp. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x8w | ||||||
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Title | The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Malonate. | ||||||
Components | METHYLGLYOXAL SYNTHASE | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / cytosol Similarity search - Function | ||||||
Biological species | THERMUS SP. GH5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Shahsavar, A. / Erfani Moghaddam, M. / Antonyuk, S.V. / Khajeh, K. / Naderi-Manesh, H. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Methylglyoxal Synthase from Thermus Sp.Gh5 in the Open and Closed Conformational States Provide Insight Into the Mechanism of Allosteric Regulation Authors: Shahsavar, A. / Erfani Moghaddam, M. / Antonyuk, S.V. / Khajeh, K. / Naderi-Manesh, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x8w.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x8w.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x8w ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x8w | HTTPS FTP |
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-Related structure data
Related structure data | 2x8v S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 14363.612 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS SP. GH5 (bacteria) / Plasmid: PET 28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B3VH91, EC: 4.2.99.11 |
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#2: Chemical | ChemComp-MLI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.78 % / Description: NONE |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: CRYSTALS WERE OBTAINED USING THE HANGING-DROP VAPOR DIFFUSION TECHNIQUE AT 21C; DROPLETS CONTAINING 8 MG/ML PROTEIN IN 0.05 M TRIS-HCL, 0.3 M NACL, 0.097 M IMIDAZOLE AND 20% OF GLYCEROL WERE ...Details: CRYSTALS WERE OBTAINED USING THE HANGING-DROP VAPOR DIFFUSION TECHNIQUE AT 21C; DROPLETS CONTAINING 8 MG/ML PROTEIN IN 0.05 M TRIS-HCL, 0.3 M NACL, 0.097 M IMIDAZOLE AND 20% OF GLYCEROL WERE EQUILIBRATED OVER WELLS CONTAINING 1 M NA MALONATE (PH 6.0). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 19, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.56 Å / Num. obs: 20151 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X8V 2x8v Resolution: 1.95→47.56 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.64 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.116 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→47.56 Å
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Refine LS restraints |
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