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Yorodumi- PDB-2wds: Crystal structure of the Streptomyces coelicolor H110A AcpS mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wds | ||||||
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Title | Crystal structure of the Streptomyces coelicolor H110A AcpS mutant in complex with cofactor CoA at 1.3 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: 1.35 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 | 2wds.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wds.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 2wds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wds_validation.pdf.gz | 728.9 KB | Display | wwPDB validaton report |
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Full document | 2wds_full_validation.pdf.gz | 729.3 KB | Display | |
Data in XML | 2wds_validation.xml.gz | 10 KB | Display | |
Data in CIF | 2wds_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wds ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wds | HTTPS FTP |
-Related structure data
Related structure data | 2jbzSC 2jcaC 2wdoC 2wdyC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14684.707 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ACETYL-COA AND COA ARE PRESENT IN THE ACTIVE SITE / 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 |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.3 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 25% PEG 2K MME WITH THE PRESENCE OF 10% PEG 400 AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.117 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 28420 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JBZ Resolution: 1.35→51.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.842 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 18.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→51.43 Å
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Refine LS restraints |
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