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Yorodumi- PDB-2jbz: Crystal structure of the Streptomyces coelicolor holo-[Acyl-carri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jbz | ||||||
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Title | Crystal structure of the Streptomyces coelicolor holo-[Acyl-carrier-protein] Synthase (AcpS) in complex with coenzyme A at 1.6 A | ||||||
Components | HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE | ||||||
Keywords | TRANSFERASE / ACP / MAGNESIUM / COENZYME A / POLIKETIDES / METAL- BINDING / LIPID SYNTHESIS / PHOSPHOPANTETHEINE ARM / FATTY ACID BIOSYNTHESIS / ACYL CARRIER PROTEIN SYNTHASE | ||||||
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: 1.62 Å | ||||||
Authors | Dall'Aglio, P. / Arthur, C. / Law, C.K.E. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jbz.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbz.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 2jbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbz ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14751.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE PROTEIN IS IN COMPLEX WITH THE COFACTOR COA / Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O86785, holo-[acyl-carrier-protein] synthase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-COA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | pH: 6.5 Details: THE PROTEIN WAS DIALYSED IN 50 MM TRIS, 10 MM MGCL2, 10% GLYCEROL, PH 8. 2.5 MM COA WAS SOAKED INTO THE PROTEIN. THE PROTEIN WAS THEN CRYSTALLYZED IN 0.3M KSCN, 15% PEG 4K, 0.1M NACACODYLATE PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 16798 / % possible obs: 90.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.88 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.15 / % possible all: 69.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: S. COELICOLOR APO- ACPS Resolution: 1.62→51.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE OCCUPANCY OF RELATIVELY DISORDERED PARTS OF THE SIDE CHAIN OF ARG15, GLU98 AND ASP111 WAS SET TO 0.5 TO GET RID OF NEGATIVE DENSITY.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→51.71 Å
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