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Yorodumi- PDB-4q3n: Crystal structure of MGS-M5, a lactate dehydrogenase enzyme from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q3n | ||||||
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Title | Crystal structure of MGS-M5, a lactate dehydrogenase enzyme from a Medee basin deep-sea metagenome library | ||||||
Components | MGS-M5 | ||||||
Keywords | HYDROLASE / metagenome / metagenomic library / ROSSMANN FOLD / DEHYDROGENASE / OXIDOREDUCTASE / L-LACTATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Stogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A. | ||||||
Citation | Journal: Environ Microbiol / Year: 2015 Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats. Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / Jebbar, M. / Jaeger, K.E. / Yakimov, M.M. / Yakunin, A.F. / Golyshin, P.N. / Golyshina, O.V. / Savchenko, A. / Ferrer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q3n.cif.gz | 150.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q3n.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q3n_validation.pdf.gz | 470.4 KB | Display | wwPDB validaton report |
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Full document | 4q3n_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 4q3n_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4q3n_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3n ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3n | HTTPS FTP |
-Related structure data
Related structure data | 4q3kC 4q3lC 4q3mC 4q3oC 1ldnS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34817.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Gene: MGS-M5 / Plasmid: p15-TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KUB4*PLUS |
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-Non-polymers , 7 types, 370 molecules
#2: Chemical | ChemComp-NA / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
-Details
Source details | THE SAMPLE HAS BEEN OBTAINED FROM LAKE MATAPAN DEEP-SEA AND IDENTIFIED |
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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: 3.15 Å3/Da / Density % sol: 60.97 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate, 0.2 M calcium acetate, 9% PEG 8K, trypsin in 1/70 molar ratio protein:trypsin cryoprotectant: 12% glycerol then paratone, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→35 Å / Num. obs: 31973 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 45.3 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 5.31 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LDN Resolution: 1.97→34.31 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→34.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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