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Yorodumi- PDB-5h3l: Structure of methylglyoxal synthase crystallised as a contaminant -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h3l | ||||||
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Title | Structure of methylglyoxal synthase crystallised as a contaminant | ||||||
Components | Methylglyoxal synthase | ||||||
Keywords | LYASE / Contaminant | ||||||
Function / homology | Methylglyoxal synthase-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hatti, K. / Dadireddy, V. / Srinivasan, N. / Ramakumar, S. / Murthy, M.R.N. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h3l.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h3l.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/5h3l ftp://data.pdbj.org/pub/pdb/validation_reports/h3/5h3l | HTTPS FTP |
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-Related structure data
Related structure data | 5h4fC 5h4gC 5h4hC 1b93S 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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-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: Escherichia coli (E. coli) #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.43 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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