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- PDB-4n4q: 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: 4n4q | ||||||
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Title | Crystal Structure of N-acetylneuraminate lyase from Mycoplasma synoviae, crystal form II | ||||||
![]() | 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 | ![]() | 242.2 KB | Display | ![]() |
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PDB format | ![]() | 195.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.3 KB | Display | ![]() |
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Full document | ![]() | 470.5 KB | Display | |
Data in XML | ![]() | 46.1 KB | Display | |
Data in CIF | ![]() | 66.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n4pSC 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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Components
#1: Protein | Mass: 33652.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50 mM MES, pH 6.0, 50 % MPD, 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 | Resolution: 2→76.718 Å / Num. all: 85882 / Num. obs: 85882 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 27.878 Å2 / Rsym value: 0.113 / Net I/σ(I): 6.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4N4P Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2827 / WRfactor Rwork: 0.2406 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7701 / SU B: 5.852 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2359 / SU Rfree: 0.2009 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.201 / 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: 54.91 Å2 / Biso mean: 27.5753 Å2 / Biso min: 8.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.054 Å / Total num. of bins used: 20
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