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- PDB-4jtl: Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jtl | ||||||
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Title | Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis | ||||||
![]() | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
![]() | TRANSFERASE / MANNO-OCTULOSONATE / SYNTHASE / LIPOPOLYSACCHARIDE / KDOP / KDO8 KDOPS / KDO8PS / TIM BARREL / LIPOPOLYSACCHARIDE BIOSYNTHESIS | ||||||
Function / homology | ![]() 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Allison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.J. | ||||||
![]() | ![]() Title: Examining the Role of Intersubunit Contacts in Catalysis by 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase. Authors: Allison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.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 | ![]() | 387.1 KB | Display | ![]() |
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PDB format | ![]() | 319.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 470.5 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jteC ![]() 4jtfC ![]() 4jtgC ![]() 4jthC ![]() 4jtiC ![]() 4jtjC ![]() 4jtkC ![]() 2qkfS 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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Unit cell |
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Components
#1: Protein | Mass: 30429.205 Da / Num. of mol.: 4 / Mutation: F139G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9JZ55, 3-deoxy-8-phosphooctulonate synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl, cryoprotectant solution, comprising 20% glycerol and reservoir ...Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl, cryoprotectant solution, comprising 20% glycerol and reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 5, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: AXCO PX70 CAPILLARY OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→38.06 Å / Num. obs: 62633 / % possible obs: 92 % / Redundancy: 3.12 % / Rmerge(I) obs: 0.08 / Χ2: 0.94 / Net I/σ(I): 7.2 / Scaling rejects: 6715 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QKF Resolution: 2.1→37.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.2124 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8057 / SU B: 11.955 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2548 / SU Rfree: 0.2005 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.54 Å2 / Biso mean: 40.4761 Å2 / Biso min: 18.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.153 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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