+Open data
-Basic information
Entry | Database: PDB / ID: 8gjh | ||||||
---|---|---|---|---|---|---|---|
Title | Salmonella ArnA | ||||||
Components | Bifunctional polymyxin resistance protein ArnA | ||||||
Keywords | OXIDOREDUCTASE / polymyxin resistance / UDP-glucuronic acid decarboxylase | ||||||
Function / homology | Function and homology information UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / lipopolysaccharide biosynthetic process / carboxy-lyase activity / lipid A biosynthetic process / response to antibiotic Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Sousa, M.C. / Mitchell, M.E. / Gatzeva-Topalova, P.Z. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2023 Title: Targeting the Conformational Change in ArnA Dehydrogenase for Selective Inhibition of Polymyxin Resistance. Authors: Mitchell, M.E. / Gatzeva-Topalova, P.Z. / Bargmann, A.D. / Sammakia, T. / Sousa, M.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gjh.cif.gz | 907.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gjh.ent.gz | 609.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gjh_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8gjh_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8gjh_validation.xml.gz | 137.5 KB | Display | |
Data in CIF | 8gjh_validation.cif.gz | 181.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/8gjh ftp://data.pdbj.org/pub/pdb/validation_reports/gj/8gjh | HTTPS FTP |
-Related structure data
Related structure data | 8ftnC 1z7eS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 73675.836 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: arnA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6FBV2 #2: Chemical | ChemComp-UGA / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.86 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.5 to 2.0 M ammonium sulfate and 0.1M MES pH 6.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.078 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→30 Å / Num. obs: 59279 / % possible obs: 95.4 % / Redundancy: 1.5 % / Biso Wilson estimate: 108.62 Å2 / Rpim(I) all: 0.098 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 1.5 % / Num. unique obs: 5929 / CC1/2: 0.525 / % possible all: 96 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z7E Resolution: 3.6→29.83 Å / SU ML: 0.5561 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.3835 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→29.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|