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- PDB-7s3u: Crystal structure of an N-acetyltransferase from Helicobacter pul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7s3u | ||||||
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Title | Crystal structure of an N-acetyltransferase from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-amino-3,6-dideoxy-D-glucose | ||||||
![]() | N-acetyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | COENZYME A / Chem-T3Q![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Griffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical investigation of an N-acetyltransferase from Helicobacter pullorum. Authors: Griffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.1 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 994.6 KB | Display | ![]() |
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Full document | ![]() | 994.7 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s3wC ![]() 7s41C ![]() 7s42C ![]() 7s43C ![]() 7s44C ![]() 7s45C ![]() 4mzuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18154.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-T3Q / [( |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16-20% PEG-3350, 200 mM KCl, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM Coenzyme A, 100 mM HEPPS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Aug 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 32307 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rsym value: 0.044 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.456→1.55 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 5844 / Rsym value: 0.214 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4mzu Resolution: 1.45→36.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.155 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 72.85 Å2 / Biso mean: 11.482 Å2 / Biso min: 4.05 Å2
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Refinement step | Cycle: final / Resolution: 1.45→36.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.486 Å / Rfactor Rfree error: 0
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