[English] 日本語
Yorodumi- PDB-7s43: Crystal structure of an N-acetyltransferase, C80T mutant, from He... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s43 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an N-acetyltransferase, C80T mutant, from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-amino-3,6-dideoxy-D-glucose | ||||||
Components | N-acetyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | COENZYME A / Chem-T3Q Function and homology information | ||||||
Biological species | Helicobacter pullorum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Griffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Protein Sci. / Year: 2021 Title: Biochemical investigation of an N-acetyltransferase from Helicobacter pullorum. Authors: Griffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7s43.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7s43.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 7s43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s43_validation.pdf.gz | 992.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7s43_full_validation.pdf.gz | 994 KB | Display | |
Data in XML | 7s43_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 7s43_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/7s43 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/7s43 | HTTPS FTP |
-Related structure data
Related structure data | 7s3uSC 7s3wC 7s41C 7s42C 7s44C 7s45C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18152.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pullorum (bacteria) / Strain: NAP8W25 / Gene: BA919_rs02330 / Production host: Escherichia coli (E. coli) |
---|
-Non-polymers , 5 types, 175 molecules
#2: Chemical | ChemComp-T3Q / [( |
---|---|
#3: Chemical | ChemComp-COA / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 11-16% 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 |
---|---|
Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jan 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 20017 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rsym value: 0.054 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3121 / Rsym value: 0.252 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7s3u Resolution: 1.7→27.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.992 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 84.25 Å2 / Biso mean: 13.722 Å2 / Biso min: 4.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→27.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|