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Yorodumi- PDB-6ifi: Crystal Structure of the Apo form of CMP-N-acetylneuraminate Synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ifi | ||||||||||||
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Title | Crystal Structure of the Apo form of CMP-N-acetylneuraminate Synthetase from Vibrio cholerae | ||||||||||||
Components | CMP-N-acetylneuraminate Synthetase | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Bacterial / CMP-sialic acid synthetase / sialic acid / CTP | ||||||||||||
Function / homology | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta Function and homology information | ||||||||||||
Biological species | Vibrio cholerae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Bose, S. / Subramanian, R. | ||||||||||||
Funding support | India, 3items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae. Authors: Bose, S. / Purkait, D. / Joseph, D. / Nayak, V. / Subramanian, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ifi.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ifi.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ifi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/6ifi ftp://data.pdbj.org/pub/pdb/validation_reports/if/6ifi | HTTPS FTP |
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-Related structure data
Related structure data | 6ifdC 1eziS 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: 28473.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: N-acylneuraminate cytidylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, calcium acetate, imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.87 Å / Num. obs: 14951 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 356 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EZI Resolution: 2.8→25.08 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.749 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.319
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Displacement parameters | Biso max: 124.23 Å2 / Biso mean: 64.35 Å2 / Biso min: 23.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→25.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 42
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