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Yorodumi- PDB-5bxx: Crystal structure of the ectoine synthase from the cold-adapted m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bxx | ||||||
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Title | Crystal structure of the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis | ||||||
Components | L-ectoine synthase | ||||||
Keywords | LYASE / Compatible solute / Osmostress protectant / Chemical chaperone / Cupin | ||||||
Function / homology | Function and homology information ectoine synthase / ectoine synthase activity / ectoine biosynthetic process Similarity search - Function | ||||||
Biological species | Sphingopyxis alaskensis RB2256 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Widderich, N. / Kobus, S. / Hoeppner, A. / Bremer, E. / Smits, S.H.J. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily. Authors: Widderich, N. / Kobus, S. / Hoppner, A. / Riclea, R. / Seubert, A. / Dickschat, J.S. / Heider, J. / Smits, S.H. / Bremer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bxx.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bxx.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 5bxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/5bxx ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bxx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16327.341 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingopyxis alaskensis RB2256 (bacteria) Gene: ectC, Sala_2951 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GNW6, ectoine synthase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion / pH: 8 Details: 0.05 M calcium acetate, 0.1 M sodium acetate pH 4.5, 40% (v/v) 1,2-propanediol, hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.3 Å / Num. obs: 38862 / % possible obs: 98.73 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.532 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→45.253 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.68 / 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: 2→45.253 Å
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Refine LS restraints |
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LS refinement shell |
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