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Yorodumi- PDB-5dcb: Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dcb | ||||||
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Title | Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / DAH7PS / Regulated / 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: 2.05 Å | ||||||
Authors | Heyes, L.C. / Parker, E.J. | ||||||
Citation | Journal: To Be Published Title: Structure of Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP at 2.05 Angstroms 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 | 5dcb.cif.gz | 542.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dcb.ent.gz | 446.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dcb_validation.pdf.gz | 516 KB | Display | wwPDB validaton report |
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Full document | 5dcb_full_validation.pdf.gz | 523.2 KB | Display | |
Data in XML | 5dcb_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 5dcb_validation.cif.gz | 81 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/5dcb ftp://data.pdbj.org/pub/pdb/validation_reports/dc/5dcb | HTTPS FTP |
-Related 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: 38712.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria) Strain: MC58 / Gene: aroG, NMB0307 / 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 , 9 types, 768 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-PEP / #8: Chemical | ChemComp-PHE / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % / Description: Monoclinic, P1211 |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 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: 7.2-7.5 |
-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: Aug 7, 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: 2.05→74.96 Å / Num. obs: 97425 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 2.05→74.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.997 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.158 / 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: 28.525 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→74.96 Å
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Refine LS restraints |
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