[English] 日本語
Yorodumi- PDB-5kdr: The crystal structure of carboxyltransferase from Staphylococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kdr | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of carboxyltransferase from Staphylococcus Aureus bound to the antimicrobial agent moiramide B. | ||||||
Components | (Acetyl-coenzyme A carboxylase carboxyl transferase subunit ...) x 2 | ||||||
Keywords | TRANSFERASE / ANTIBIOTIC / MOIRAMIDE B / acetyl-CoA carboxylase / carboxyltransferase / enolate | ||||||
Function / homology | Function and homology information acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Silvers, M.A. / Pakhomova, S. / Neau, D. / Silvers, W.C. / Anzalone, N. / Taylor, C.M. / Waldrop, G.L. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B. Authors: Silvers, M.A. / Pakhomova, S. / Neau, D.B. / Silvers, W.C. / Anzalone, N. / Taylor, C.M. / Waldrop, G.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kdr.cif.gz | 233.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kdr.ent.gz | 186.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kdr_validation.pdf.gz | 737.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5kdr_full_validation.pdf.gz | 741.4 KB | Display | |
Data in XML | 5kdr_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 5kdr_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdr ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdr | HTTPS FTP |
-Related structure data
Related structure data | 2f9iS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Acetyl-coenzyme A carboxylase carboxyl transferase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36684.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria) Strain: USA300 / Gene: accA, SAUSA300_1646 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2FG38, UniProt: Q2FXM7*PLUS, acetyl-CoA carboxylase |
---|---|
#2: Protein | Mass: 31916.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / Gene: accD, SAB1559c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2YTE0, UniProt: Q2FXM6*PLUS, acetyl-CoA carboxylase |
-Non-polymers , 5 types, 27 molecules
#3: Chemical | #4: Chemical | ChemComp-YT5 / | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.61 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES, 1.6 M NH4SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2016 / Details: KB mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 23238 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / % possible all: 98.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F9I Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU B: 33.226 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R: 0.582 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.113 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|