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Yorodumi- PDB-2jca: Crystal structure of the streptomyces coelicolor holo- [Acyl-carr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jca | ||||||
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Title | Crystal structure of the streptomyces coelicolor holo- [Acyl-carrier-protein] Synthase (AcpS) at 2 A. | ||||||
Components | HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE | ||||||
Keywords | TRANSFERASE / ACP / MAGNESIUM / POLIKETIDE / 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: 1.98 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jca.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jca.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jca_validation.pdf.gz | 466.4 KB | Display | wwPDB validaton report |
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Full document | 2jca_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 2jca_validation.xml.gz | 18 KB | Display | |
Data in CIF | 2jca_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jca ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jca | HTTPS FTP |
-Related structure data
Related structure data | 2jbzC 2wdoC 2wdsC 2wdyC 1f7tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 14751.777 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source 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 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.78 % |
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Crystal grow | pH: 8.8 Details: ACPS WAS DIALYZED IN 50 MM TRIS PH 8.8, 10% GLYCEROL. THEN IT WAS CRYSTALLIZED IN 0.2M AMMONIUM SULPHATE, 0.1M NACACODYLATE PH 6.5, 30% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.48 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.48 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 25759 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.19 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.04 / % possible all: 95.7 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F7T Resolution: 1.98→65.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.791 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY IN THE B CHAIN BETWEEN RESIDUES 65-68 IS NOT WELL DEFINED. THE ELECTRON DENSITY IN THE B CHAIN BETWEEN RESIDUES 22-25 IS NOT WELL DEFINED.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→65.8 Å
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