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Yorodumi- PDB-5suv: Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5suv | ||||||
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Title | Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria meningitidis in complex with Coenzyme A | ||||||
Components | Holo-[acyl-carrier-protein] synthase | ||||||
Keywords | TRANSFERASE / acpS / FASII / trimer / CoA | ||||||
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 | Neisseria meningitidis FAM18 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Nanson, J.D. / Forwood, J.K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria meningitidis in complex with Coenzyme A Authors: Nanson, J.D. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5suv.cif.gz | 244.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5suv.ent.gz | 203.7 KB | Display | PDB format |
PDBx/mmJSON format | 5suv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5suv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5suv_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5suv_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 5suv_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/5suv ftp://data.pdbj.org/pub/pdb/validation_reports/su/5suv | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 13765.921 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis FAM18 (bacteria) Strain: ATCC 700532 / DSM 15464 / FAM18 / Gene: acpS, NMC1700 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) References: UniProt: A1KVH5, holo-[acyl-carrier-protein] synthase #2: Chemical | #3: 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: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium citrate tribasic, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.951 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.951 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.343 Å / Num. obs: 41271 / % possible obs: 98.2 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.895 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.343 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.343 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.5811 Å / Origin y: 92.9984 Å / Origin z: 3.2134 Å
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Refinement TLS group | Selection details: all |