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Yorodumi- PDB-6ckk: N. meningitidis CMP-sialic acid synthetase in the presence of CTP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ckk | ||||||
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Title | N. meningitidis CMP-sialic acid synthetase in the presence of CTP and Ca2+ | ||||||
Components | N-acylneuraminate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / polysaccharide synthesis / sialic acid-activator / CMP-transferase | ||||||
Function / homology | Function and homology information N-acylneuraminate cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Matthews, M.M. / Fisher, A.J. / Chen, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Catalytic Cycle ofNeisseria meningitidisCMP-Sialic Acid Synthetase Illustrated by High-Resolution Protein Crystallography. Authors: Matthews, M.M. / McArthur, J.B. / Li, Y. / Yu, H. / Chen, X. / Fisher, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ckk.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ckk.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ckk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ckk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ckk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ckk_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 6ckk_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/6ckk ftp://data.pdbj.org/pub/pdb/validation_reports/ck/6ckk | HTTPS FTP |
-Related structure data
Related structure data | 6ckjC 6cklC 6ckmC 1eyrS 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: 24920.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: neuA, siaB, synB / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) References: UniProt: P0A0Z8, N-acylneuraminate cytidylyltransferase #2: Chemical | #3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 46.93 % / Description: rectangular |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M imidazole pH 8, 6% PEG 8000, and 0.2M calcium acetate Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03316 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03316 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→79.11 Å / Num. obs: 42666 / % possible obs: 93.8 % / Redundancy: 3.35 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.64 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 2883 / CC1/2: 0.92 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EYR Resolution: 1.8→79.11 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / 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: 22.468 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→79.11 Å
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Refine LS restraints |
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