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- PDB-4n4p: Crystal Structure of N-acetylneuraminate lyase from Mycoplasma sy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n4p | ||||||
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Title | Crystal Structure of N-acetylneuraminate lyase from Mycoplasma synoviae, crystal form I | ||||||
![]() | Acylneuraminate lyase | ||||||
![]() | LYASE / TIM barrel | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Georgescauld, F. / Popova, K. / Gupta, A.J. / Bracher, A. / Engen, J.R. / Hayer-Hartl, M. / Hartl, F.U. | ||||||
![]() | ![]() Title: GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding. Authors: Georgescauld, F. / Popova, K. / Gupta, A.J. / Bracher, A. / Engen, J.R. / Hayer-Hartl, M. / Hartl, F.U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.8 KB | Display | ![]() |
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PDB format | ![]() | 207.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 51.2 KB | Display | |
Data in CIF | ![]() | 77.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n4qC ![]() 1f5zS C: citing same article ( S: Starting model for refinement |
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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: 33652.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50 mM MES, pH 6.0, 4 % MPD, 0.2 M NaCl, 35 % PEG 400, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.89997 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 12.9 % / Av σ(I) over netI: 3.6 / Number: 1527148 / Rsym value: 0.176 / D res high: 1.803 Å / D res low: 103.016 Å / Num. obs: 118560 / % possible obs: 99.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.8→30 Å / Num. all: 113552 / Num. obs: 112371 / % possible obs: 98.96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.808 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 87.52 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1F5Z Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1961 / WRfactor Rwork: 0.1643 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.887 / SU B: 2.273 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1218 / SU Rfree: 0.1157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.46 Å2 / Biso mean: 15.5743 Å2 / Biso min: 4.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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