[English] 日本語
Yorodumi- PDB-2wdy: Crystal structure of the Streptomyces coelicolor D111A AcpS mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wdy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Streptomyces coelicolor D111A AcpS mutant in complex with cofactor CoA at 1.4 A | ||||||
Components | HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE | ||||||
Keywords | TRANSFERASE / PHOSPHOPANTETHEINE ARM / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / POLYKETIDES | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOMYCES COELICOLOR (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Dall'Aglio, P. / Arthur, C. / Crump, M.P. / Crosby, J. / Hadfield, A.T. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Analysis of Streptomyces Coelicolor Phosphopantetheinyl Transferase, Acps, Reveals the Basis for Relaxed Substrate Specificity. Authors: Dall'Aglio, P. / Arthur, C. / Williams, C. / Vasilakis, K. / Maple, H.J. / Crosby, J. / Crump, M.P. / Hadfield, A.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wdy.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wdy.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wdy_validation.pdf.gz | 991.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wdy_full_validation.pdf.gz | 995.8 KB | Display | |
Data in XML | 2wdy_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 2wdy_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wdy ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wdy | HTTPS FTP |
-Related structure data
Related structure data | 2jbzSC 2jcaC 2wdoC 2wdsC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14707.768 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MG AND COA ARE PRESENT IN THE ACTIVE SITE. INSPECTION OF THE ELECTRON DENSITY SUGGESTS COA BINDS IN 2 ALTERNATIVE CONFORMATIONS. Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O86785, holo-[acyl-carrier-protein] synthase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-COA / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.2 M POTASSIUM THIOCYANATE, 0.1 M SODIUM CACODYLATE PH 6.5, 8% PEG 20K PLUS 8% PEG 550 MME, 15% GLYCEROL WAS THEN ADDED AS CRYO |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.953 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 25707 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 96.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JBZ Resolution: 1.4→51.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.096 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA WAS BOUND IN TWO ALTERNATIVE CONFORMATIONS. WHILST THE ELECTRON DENSITY FOR THE ADENINE RINGS OF BOTH COAS, INCLUDING THE PHOSPHATES, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA WAS BOUND IN TWO ALTERNATIVE CONFORMATIONS. WHILST THE ELECTRON DENSITY FOR THE ADENINE RINGS OF BOTH COAS, INCLUDING THE PHOSPHATES, AND THEIR RELATED MAGNESIUM IONS WAS VERY CLEAR, THE DENSITY FOR THE PHOSPHOPANTETHEINE ARMS WAS NOT WELL DEFINED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.166 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→51.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|