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Yorodumi- PDB-5wxx: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate ra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wxx | |||||||||||||||
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Title | Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with citrate | |||||||||||||||
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 / : / CITRIC ACID / McyF Function and homology information | |||||||||||||||
Biological species | Microcystis aeruginosa PCC 7806 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | |||||||||||||||
Authors | Cao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z. | |||||||||||||||
Funding support | China, 4items
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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 | 5wxx.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wxx.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 5wxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/5wxx ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wxx | HTTPS FTP |
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-Related 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: 29480.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria) Gene: mcyF, IPF_371 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RNB4 |
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#2: Chemical | ChemComp-CIT / |
#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: 3.91 Å3/Da / Density % sol: 68.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% (w/v) polyethylene glycol 3350, 0.1 M sodium citrate, pH 6.5, 0.2 magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: a liquid-nitrogen-gas stream |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→111.5 Å / Num. obs: 18567 / % possible obs: 99.9 % / Redundancy: 12.7 % / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 2.35→2.39 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→42.667 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.621 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.978 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→42.667 Å
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Refine LS restraints |
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