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Yorodumi- PDB-5xnk: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate ra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xnk | ||||||
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Title | Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with DL-methyl-aspartate | ||||||
Components | McyF | ||||||
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 / (2S,3S)-3-methyl-aspartic acid / 3-METHYL-BETA-D-ASPARTIC ACID / McyF Function and homology information | ||||||
Biological species | Microcystis aeruginosa PCC 7806 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Cao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z. | ||||||
Citation | Journal: To Be Published Title: Structure-function Analyses of a Cyanobacterial Aspartate Racemase Reveal Its Catalytic Mechanism and Substrate Specificity Authors: Cao, D.D. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xnk.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xnk.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/5xnk ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xnk | HTTPS FTP |
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-Related structure data
Related structure data | 5wxxS 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
#1: Protein | Mass: 29229.668 Da / Num. of mol.: 1 / Mutation: C87S 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-2AS / ( |
#3: Chemical | ChemComp-ACB / |
#4: 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: 3.61 Å3/Da / Density meas: 34.76 Mg/m3 / Density % sol: 65.93 % |
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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: BL19U1 / Wavelength: 0.97775 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→111.76 Å / Num. obs: 5683 / % possible obs: 96.1 % / Redundancy: 4.8 % / Net I/σ(I): 9.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WXX Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.046 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / 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: 85.789 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→50 Å
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Refine LS restraints |
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