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Yorodumi- PDB-4jtj: Crystal structure of R117K mutant of 3-deoxy-D-manno-octulosonate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jtj | ||||||
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Title | Crystal structure of R117K mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / MANNO-OCTULOSONATE / SYNTHASE / LIPOPOLYSACCHARIDE / KDOP / KDO8 KDOPS / KDO8PS / TIM BARREL / LIPOPOLYSACCHARIDE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 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 | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Allison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.J. | ||||||
Citation | Journal: Biochemistry / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jtj.cif.gz | 398.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jtj.ent.gz | 329.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jtj_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 4jtj_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 4jtj_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 4jtj_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/4jtj ftp://data.pdbj.org/pub/pdb/validation_reports/jt/4jtj | HTTPS FTP |
-Related structure data
Related structure data | 4jteC 4jtfC 4jtgC 4jthC 4jtiC 4jtkC 4jtlC 2qkfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30491.314 Da / Num. of mol.: 4 / Mutation: R117K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: kdsA, NMB1283 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9JZ55, 3-deoxy-8-phosphooctulonate synthase #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.07 % |
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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 20% glycerol and 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 0.6-3.0 M NaCl, cryoprotectant 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.75→39.93 Å / Num. obs: 113642 / % possible obs: 98.8 % / Redundancy: 4.07 % / Rmerge(I) obs: 0.041 / Χ2: 0.97 / Net I/σ(I): 14.1 / Scaling rejects: 3495 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QKF Resolution: 1.75→39.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1965 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8525 / SU B: 5.068 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1168 / SU Rfree: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112 / 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: 100.94 Å2 / Biso mean: 35.9257 Å2 / Biso min: 17.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→39.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.794 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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