+Open data
-Basic information
Entry | Database: PDB / ID: 5huh | ||||||
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Title | Crystal Structure of NadE from Streptococcus pyogenes | ||||||
Components | NH(3)-dependent NAD(+) synthetase | ||||||
Keywords | TRANSFERASE / NAD Synthetase | ||||||
Function / homology | Function and homology information NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes serotype M49 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Booth, W.T. / Chruszcz, M. | ||||||
Citation | Journal: FEBS J. / Year: 2017 Title: Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD(+) synthetase. Authors: Booth, W.T. / Morris, T.L. / Mysona, D.P. / Shah, M.J. / Taylor, L.K. / Karlin, T.W. / Clary, K. / Majorek, K.A. / Offermann, L.R. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5huh.cif.gz | 218.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5huh.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 5huh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/5huh ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5huh | HTTPS FTP |
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-Related structure data
Related structure data | 5hujC 5hulC 5huoC 5hupC 3hmqS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 9 - 282 / Label seq-ID: 34 - 307
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-Components
#1: Protein | Mass: 33877.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M49 (strain NZ131) (bacteria) Strain: NZ131 / Gene: nadE, Spy49_1281c / Plasmid: pjExpress411 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3BZ89, NAD+ synthase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.19 Å3/Da / Density % sol: 43.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 20% PEG 4000, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 19874 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.5 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3hmq Resolution: 2.5→43.72 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.166 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.282 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.869 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→43.72 Å
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Refine LS restraints |
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