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Yorodumi- PDB-5d09: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d09 | ||||||
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Title | Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala variant | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / DAH7PS / Allostery | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Heyes, L.C. / Parker, E.J. | ||||||
Citation | Journal: To Be Published Title: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala variant at 2.35 Angstroms resolution Authors: Heyes, L.C. / 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 | 5d09.cif.gz | 511.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d09.ent.gz | 422.5 KB | Display | PDB format |
PDBx/mmJSON format | 5d09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/5d09 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/5d09 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38636.039 Da / Num. of mol.: 4 / Mutation: F211A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria) Strain: MC58 / Gene: aroG, NMB0307 / Plasmid: pT7-7 / Cell line (production host): BL21* / Production host: Escherichia coli (E. coli) References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 6 types, 343 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PEP / | #4: Chemical | ChemComp-TMO / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % / Description: Orthorhombic, P212121 |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1M Tris HCl pH 7.3, 0.2 M trimethyl-amino-N-oxide (TMAO), 0.4 mM MnSO4 and PEG 2000MME PH range: 7.3 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→100.45 Å / Num. obs: 67384 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.35→100.45 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.377 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 mean: 44.75 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→100.45 Å
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Refine LS restraints |
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