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Yorodumi- PDB-7w58: Crystal structure of acyl-carrier protein synthase from Mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w58 | ||||||
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Title | Crystal structure of acyl-carrier protein synthase from Mycobacterium smegmatis | ||||||
Components | 4'-phosphopantetheinyl transferase | ||||||
Keywords | TRANSFERASE / AcpS / Mycobacterium smegmatis | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å | ||||||
Authors | Yadav, S. / Bhatia, I. / Biswal, B.K. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously. Authors: Bhatia, I. / Yadav, S. / Biswal, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w58.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w58.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 7w58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w58_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7w58_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7w58_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7w58_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w58 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w58 | HTTPS FTP |
-Related structure data
Related structure data | 3gwmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 14186.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: acpS, NCTC7017_04197 / Production host: Mycolicibacterium smegmatis (bacteria) References: UniProt: A0A8B4R1L0, holo-[acyl-carrier-protein] synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium acetate trihydrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5417 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 6746 / % possible obs: 97.5 % / Redundancy: 8.3 % / CC1/2: 0.99 / Net I/σ(I): 21.44 |
Reflection shell | Resolution: 2.25→2.29 Å / Num. unique obs: 180 / CC1/2: 0.81 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GWM Resolution: 2.27→34.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.128 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.61 Å2 / Biso mean: 34.874 Å2 / Biso min: 16.04 Å2
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Refinement step | Cycle: final / Resolution: 2.27→34.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.271→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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