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- PDB-4jth: Crystal structure of F114R/R117Q mutant of 3-deoxy-D-manno-octulo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jth | ||||||
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Title | Crystal structure of F114R/R117Q 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 | ![]() | 412.3 KB | Display | ![]() |
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PDB format | ![]() | 339.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4jteC ![]() 4jtfC ![]() 4jtgC ![]() 4jtiC ![]() 4jtjC ![]() 4jtkC ![]() 4jtlC ![]() 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: 30500.279 Da / Num. of mol.: 4 / Mutation: F114R, R117Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9JZ55, 3-deoxy-8-phosphooctulonate synthase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-GOL / | #5: 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: 47.9 % |
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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 1.6 M NaCl. cryoprotectant 20% glycerol and the reservoir solution, Vapor ...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 1.6 M NaCl. cryoprotectant 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→45.955 Å / Num. all: 78806 / Num. obs: 78806 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.115 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→45.955 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.1647 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8956 / SU B: 5.914 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1524 / SU Rfree: 0.1357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.136 / 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: 100.06 Å2 / Biso mean: 28.1477 Å2 / Biso min: 10.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.955 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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