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- PDB-6ckl: N. meningitidis CMP-sialic acid synthetase in the presence of CMP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ckl | ||||||
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Title | N. meningitidis CMP-sialic acid synthetase in the presence of CMP and Neu5Ac2en | ||||||
![]() | N-acylneuraminate cytidylyltransferase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matthews, M.M. / Fisher, A.J. / Chen, X. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.2 KB | Display | ![]() |
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PDB format | ![]() | 114.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ckjC ![]() 6ckkC ![]() 6ckmC ![]() 1eyrS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 1 - 225 / Label seq-ID: 1 - 225
NCS ensembles :
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Components
-Protein / Sugars , 2 types, 6 molecules ABC![](data/chem/img/DAN.gif)
![](data/chem/img/DAN.gif)
#1: Protein | ![]() Mass: 24920.408 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P0A0Z8, ![]() #4: Sugar | |
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-Non-polymers , 4 types, 119 molecules ![](data/chem/img/C5P.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.06 % / Description: thick needles |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium citrate/citric acid pH 5.5 and 20% PEG 3000 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.68→97.86 Å / Num. obs: 22814 / % possible obs: 97.1 % / Redundancy: 3.14 % / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.57 |
Reflection shell | Resolution: 2.68→2.75 Å / Redundancy: 2.78 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 1615 / CC1/2: 0.727 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1EYR Resolution: 2.684→97.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 12.529 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / 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: 43.447 Å2
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Refinement step | Cycle: 1 / Resolution: 2.684→97.86 Å
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Refine LS restraints |
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