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- PDB-5h3l: Structure of methylglyoxal synthase crystallised as a contaminant -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h3l | ||||||
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Title | Structure of methylglyoxal synthase crystallised as a contaminant | ||||||
![]() | Methylglyoxal synthase | ||||||
![]() | LYASE / Contaminant | ||||||
Function / homology | Methylglyoxal synthase-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hatti, K. / Dadireddy, V. / Srinivasan, N. / Ramakumar, S. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structure determination of contaminant proteins using the MarathonMR procedure. Authors: Hatti, K. / Biswas, A. / Chaudhary, S. / Dadireddy, V. / Sekar, K. / Srinivasan, N. / Murthy, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.6 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h4fC ![]() 5h4gC ![]() 5h4hC ![]() 1b93S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16958.518 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5M Sodium formate.HCl, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→61.16 Å / Num. all: 30046 / Num. obs: 29980 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.991 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 14.6 % / Rmerge(I) obs: 2.179 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.436 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B93 Resolution: 2.1→61.165 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→61.165 Å
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Refine LS restraints |
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LS refinement shell |
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