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Yorodumi- PDB-5d03: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d03 | ||||||
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Title | Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Val223Ala 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: 1.84 Å | ||||||
Authors | Heyes, L.C. / Parker, E.J. | ||||||
Citation | Journal: To Be Published Title: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Val223Ala variant at 1.84 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 | 5d03.cif.gz | 521.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d03.ent.gz | 428.5 KB | Display | PDB format |
PDBx/mmJSON format | 5d03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d03_validation.pdf.gz | 498.1 KB | Display | wwPDB validaton report |
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Full document | 5d03_full_validation.pdf.gz | 502.5 KB | Display | |
Data in XML | 5d03_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 5d03_validation.cif.gz | 77.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/5d03 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/5d03 | HTTPS FTP |
-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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Details | Tetramer by Analytical Gel filtration |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38684.082 Da / Num. of mol.: 4 / Mutation: V223A 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 , 7 types, 749 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PEP / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % / Description: Monoclinic, P1211 |
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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: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 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: 1.84→75.53 Å / Num. obs: 126857 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.4 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Resolution: 1.84→75.53 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.197 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / 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: 33.103 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→75.53 Å
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