[English] 日本語
Yorodumi- PDB-7trr: Structure of Neisseria gonorrhoeae peptidoglycan O-acetyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7trr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Neisseria gonorrhoeae peptidoglycan O-acetyltransferase B (PatB) with methylsulfonyl adduct | |||||||||
Components | Peptidoglycan O-acetyltransferase B | |||||||||
Keywords | TRANSFERASE / Peptidoglycan / O-acetyltransferase / Neisseria / gonorrhoeae | |||||||||
Function / homology | Protein of unknown function DUF459 / Protein of unknown function (DUF459) / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / methanesulfonic acid / Periplasmic protein Function and homology information | |||||||||
Biological species | Neisseria gonorrhoeae FA 1090 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8000158121 Å | |||||||||
Authors | Brott, A.S. / Stangherlin, S. / Clarke, A.J. | |||||||||
Funding support | Canada, 2items
| |||||||||
Citation | Journal: To Be Published Title: Structure of Neisseria gonorrhoeae peptidoglycan O-acetyltransferase B (PatB) Authors: Brott, A.S. / Stangherlin, S. / Clarke, A.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7trr.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7trr.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 7trr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7trr_validation.pdf.gz | 710.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7trr_full_validation.pdf.gz | 711 KB | Display | |
Data in XML | 7trr_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 7trr_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/7trr ftp://data.pdbj.org/pub/pdb/validation_reports/tr/7trr | HTTPS FTP |
-Related structure data
Related structure data | 7tjbC 7tlvSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 25437.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria) Strain: ATCC 700825 / FA 1090 / Gene: NGO_0533 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5F966 |
---|---|
#2: Chemical | ChemComp-03S / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.08 M ammonium sulfate in 0.1 M phosphate-citrate buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97828 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97828 Å / Relative weight: 1 |
Reflection | Resolution: 1.41997→72.85 Å / Num. obs: 58729 / % possible obs: 100 % / Redundancy: 32 % / Biso Wilson estimate: 22.70018156 Å2 / CC1/2: 0.996 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 1.43→1.47 Å / Num. unique obs: 4786 / CC1/2: 0.44 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TLV Resolution: 1.8000158121→49.1500006166 Å / SU ML: 0.210577724527 / Cross valid method: THROUGHOUT / σ(F): 1.36300540135 / Phase error: 23.437185808 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2026547367 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8000158121→49.1500006166 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|