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Yorodumi- PDB-5xuh: Crystal structure of Escherichia coli holo-[acyl-carrier-protein]... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xuh | ||||||
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Title | Crystal structure of Escherichia coli holo-[acyl-carrier-protein] synthase (AcpS) D9A mutant in complex with CoA | ||||||
Components | Holo-[acyl-carrier-protein] synthase | ||||||
Keywords | TRANSFERASE / Gram-negative bacteria / phosphopantetheinyl transferase / homotrimer | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / transferase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structures of acyl carrier protein synthases (AcpS) from three Gram-negative bacteria Authors: Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xuh.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xuh.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xuh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5xuh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5xuh_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 5xuh_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/5xuh ftp://data.pdbj.org/pub/pdb/validation_reports/xu/5xuh | HTTPS FTP |
-Related structure data
Related structure data | 5xu7C 5xukC 5xumC 3qmnS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 14030.287 Da / Num. of mol.: 3 / Mutation: D9A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acpS, dpj, b2563, JW2547 / Production host: Escherichia coli (E. coli) References: UniProt: P24224, holo-[acyl-carrier-protein] synthase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / | #4: Chemical | #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: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl pH 8.0, 18% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2014 |
Radiation | Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→48.9 Å / Num. obs: 30966 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.02→2.13 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 8 / Num. unique obs: 4449 / Rpim(I) all: 0.113 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QMN Resolution: 2.02→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.037 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.749 Å2
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Refinement step | Cycle: 1 / Resolution: 2.02→30 Å
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Refine LS restraints |
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