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- PDB-3qq0: Crystal structure of a deletion mutant (N59) of 3-deoxy-D-manno-o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qq0 | ||||||
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Title | Crystal structure of a deletion mutant (N59) 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 / BIOSYNTHESIS / LYASE / 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. / Jameson, G.B. / Parker, E.J. | ||||||
![]() | ![]() Title: Targeting the role of a key conserved motif for substrate selection and catalysis by 3-deoxy-D-manno-octulosonate 8-phosphate synthase Authors: Allison, T.M. / Hutton, R.D. / Cochrane, F.C. / Yeoman, J.A. / 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 | ![]() | 407.6 KB | Display | ![]() |
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PDB format | ![]() | 335.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.8 KB | Display | ![]() |
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Full document | ![]() | 485 KB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 63.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qpyC ![]() 3qpzC ![]() 3qq1C ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 30405.229 Da / Num. of mol.: 4 / Mutation: DEL(N59) 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 | #4: Chemical | #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: 47.88 % |
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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. Immediately prior to data collection, crystals were harvested and ...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. Immediately prior to data collection, crystals were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 14, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.9→36.66 Å / Num. all: 91249 / Num. obs: 91249 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.52 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QKF Resolution: 1.9→32.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2303 / WRfactor Rwork: 0.1891 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8558 / SU B: 7.076 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1434 / SU Rfree: 0.1365 / Cross valid method: THROUGHOUT / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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: 87.03 Å2 / Biso mean: 28.93 Å2 / Biso min: 11.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1564 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.897→1.946 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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