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Yorodumi- PDB-7q93: Crystal Structure of Agrobacterium tumefaciens NADQ, NAD complex. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q93 | ||||||
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Title | Crystal Structure of Agrobacterium tumefaciens NADQ, NAD complex. | ||||||
Components | NADQ transcription factor | ||||||
Keywords | TRANSCRIPTION / NADQ / Transcription factor / ATP / NAD / NUDIX domain / WHTH domain / DNA binding / selenium phasing | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.19 Å | ||||||
Authors | Cianci, M. / Minazzato, G. / Heroux, A. / Raffaelli, N. / Sorci, L. / Gasparrini, M. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2022 Title: Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis. Authors: Minazzato, G. / Gasparrini, M. / Heroux, A. / Sernova, N.V. / Rodionov, D.A. / Cianci, M. / Sorci, L. / Raffaelli, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q93.cif.gz | 292.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q93.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q93_validation.pdf.gz | 1003.8 KB | Display | wwPDB validaton report |
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Full document | 7q93_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7q93_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 7q93_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/7q93 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/7q93 | HTTPS FTP |
-Related structure data
Related structure data | 7q91C 7q92C 7q94C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38748.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Selenated version Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu4099 / Plasmid: pET100 / Cell line (production host): B834(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): MET- / References: UniProt: A9CG24 #2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM Bis-tris-propane, 250 mM sodium potassium tartrate, 24 % (w/v) PEG 3400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→86.17 Å / Num. obs: 67319 / % possible obs: 98.7 % / Redundancy: 2 % / Biso Wilson estimate: 41.1 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.06162 / Rrim(I) all: 0.08714 / Net I/σ(I): 10.27 |
Reflection shell | Resolution: 2.19→2.268 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4347 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6657 / CC1/2: 0.68 / CC star: 0.9 / Rrim(I) all: 0.6147 / % possible all: 98.27 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: native structure Resolution: 2.19→86.17 Å / SU ML: 0.302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6753 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→86.17 Å
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Refine LS restraints |
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LS refinement shell |
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