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Yorodumi- PDB-4jtf: Crystal structure of F114R mutant of 3-deoxy-D-manno-octulosonate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jtf | ||||||
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Title | Crystal structure of F114R 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 / BIOSYNTHESIS / 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: 1.8 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 | 4jtf.cif.gz | 402.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jtf.ent.gz | 332.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jtf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jtf_validation.pdf.gz | 472.6 KB | Display | wwPDB validaton report |
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Full document | 4jtf_full_validation.pdf.gz | 486.3 KB | Display | |
Data in XML | 4jtf_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 4jtf_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/4jtf ftp://data.pdbj.org/pub/pdb/validation_reports/jt/4jtf | HTTPS FTP |
-Related structure data
Related structure data | 4jteC 4jtgC 4jthC 4jtiC 4jtjC 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: 30529.346 Da / Num. of mol.: 4 / Mutation: F114R 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-CL / #4: Chemical | ChemComp-NA / | #5: 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: 2.33 Å3/Da / Density % sol: 47.27 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 19, 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: 1.8→39.7 Å / Num. obs: 105281 / % possible obs: 98.7 % / Redundancy: 4.19 % / Rmerge(I) obs: 0.044 / Χ2: 0.93 / Net I/σ(I): 12.6 / Scaling rejects: 3331 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→39.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2148 / WRfactor Rwork: 0.1859 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8678 / SU B: 4.785 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1212 / SU Rfree: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115 / 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: 98.39 Å2 / Biso mean: 33.9468 Å2 / Biso min: 17.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 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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