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Yorodumi- PDB-5wxy: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate ra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wxy | ||||||
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Title | Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with L-aspartate | ||||||
Components | McyFAspartate racemase | ||||||
Keywords | ISOMERASE / aspartate racemase / McyF / microcystin | ||||||
Function / homology | racemase activity, acting on amino acids and derivatives / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / : / ASPARTIC ACID / McyF Function and homology information | ||||||
Biological species | Microcystis aeruginosa PCC 7806 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Cao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural insights into the catalysis and substrate specificity of cyanobacterial aspartate racemase McyF. Authors: Cao, D.D. / Zhang, C.P. / Zhou, K. / Jiang, Y.L. / Tan, X.F. / Xie, J. / Ren, Y.M. / Chen, Y. / Zhou, C.Z. / Hou, W.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wxy.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wxy.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/5wxy ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wxy | HTTPS FTP |
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-Related structure data
Related structure data | 5wxxSC 5wxzC 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: 29213.605 Da / Num. of mol.: 1 / Mutation: C87S, C195S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria) Gene: mcyF, IPF_371 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RNB4 |
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#2: Chemical | ChemComp-ASP / |
#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: 3.83 Å3/Da / Density % sol: 67.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 25% (w/v) polyethylene glycol 3350, 0.2 magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97791 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→111.27 Å / Num. obs: 12847 / % possible obs: 99.7 % / Redundancy: 7.8 % / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.63→2.68 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WXX Resolution: 2.63→41.831 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.841 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.214 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.949 Å2
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Refinement step | Cycle: 1 / Resolution: 2.63→41.831 Å
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Refine LS restraints |
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