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Yorodumi- PDB-5dce: Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dce | ||||||
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Title | Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated (Tryptophan) | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / Allostery / aromatic amino acids / DAH7PS | ||||||
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: 2.23 Å | ||||||
Authors | Heyes, L.C. / Parker, E.J. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: The Functional Unit of Neisseria meningitidis 3-Deoxy--Arabino-Heptulosonate 7-Phosphate Synthase Is Dimeric. Authors: Cross, P.J. / Heyes, L.C. / Zhang, S. / Nazmi, A.R. / 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 | 5dce.cif.gz | 526.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dce.ent.gz | 434.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/5dce ftp://data.pdbj.org/pub/pdb/validation_reports/dc/5dce | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#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 / Plasmid: PT7-7 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-TRP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % / 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: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→75.37 Å / Num. obs: 72956 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.23→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.23→75.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.469 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.213 / 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: 56.745 Å2
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Refinement step | Cycle: 1 / Resolution: 2.23→75.37 Å
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Refine LS restraints |
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