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- PDB-5xnj: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate/gl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xnj | ||||||
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Title | Crystal structure of Microcystis aeruginosa PCC 7806 aspartate/glutamate racemase in complex with L-glutamate | ||||||
![]() | McyF | ||||||
![]() | ISOMERASE / aspartate/glutamate racemase / McyF / microcystin | ||||||
Function / homology | racemase activity, acting on amino acids and derivatives / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / GLUTAMIC ACID / McyF![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z. | ||||||
![]() | ![]() Title: Structure-function Analyses of a Cyanobacterial Aspartate/Glutamate 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60 KB | Display | ![]() |
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PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.5 KB | Display | ![]() |
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Full document | ![]() | 431.6 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xniC ![]() 5wxxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Gene: mcyF, IPF_371 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GLU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.35 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.82→111.93 Å / Num. obs: 10438 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Χ2: 1.402 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WXX Resolution: 2.82→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.201 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.258 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 135.6 Å2 / Biso mean: 68.508 Å2 / Biso min: 43.82 Å2
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Refinement step | Cycle: final / Resolution: 2.82→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.817→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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