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- PDB-7q94: Crystal Structure of Agrobacterium tumefaciens NADQ, DNA complex. -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q94 | ||||||
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Title | Crystal Structure of Agrobacterium tumefaciens NADQ, DNA complex. | ||||||
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![]() | TRANSCRIPTION / NADQ / Transcription factor / ATP / NAD / NUDIX domain / WHTH domain / DNA binding / selenium phasing | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cianci, M. / Minazzato, G. / Heroux, A. / Raffaelli, N. / Sorci, L. / Gasparrini, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180 KB | Display | ![]() |
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PDB format | ![]() | 118.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7q91C ![]() 7q92C ![]() 7q93C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38373.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: Atu4099 / Plasmid: pET100 / Production host: ![]() ![]() #2: DNA chain | | Mass: 9814.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | | Mass: 9863.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES, mM lithium chloride, 28% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 4.3→77.65 Å / Num. obs: 6399 / % possible obs: 99.63 % / Redundancy: 2 % / Biso Wilson estimate: 169.05 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.08082 / Rrim(I) all: 0.1143 / Net I/σ(I): 7.14 |
Reflection shell | Resolution: 4.3→4.455 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7835 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 627 / CC star: 0.645 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: native monomer Resolution: 4.3→77.65 Å / SU ML: 0.367 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 43.9391 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: 177.77 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.3→77.65 Å
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Refine LS restraints |
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LS refinement shell |
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