+Open data
-Basic information
Entry | Database: PDB / ID: 7pp7 | |||||||||
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Title | Thunberia alata 16:0-ACP desaturase | |||||||||
Components | Acyl-[acyl-carrier-protein] 6-desaturase | |||||||||
Keywords | OXIDOREDUCTASE / Desaturase / di-iron protein | |||||||||
Function / homology | Function and homology information acyl-[acyl-carrier-protein] 6-desaturase / stearoyl-[ACP] desaturase activity / chloroplast / fatty acid biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Thunbergia alata (black-eyed Susan vine) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Guy, J.E. / Whittle, E. / Cai, Y. / Chai, J. / Lindqvist, Y. / Shanklin, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Plant Physiol. / Year: 2022 Title: Regioselectivity mechanism of the Thunbergia alata Delta 6-16:0-acyl carrier protein desaturase. Authors: Guy, J.E. / Cai, Y. / Baer, M.D. / Whittle, E. / Chai, J. / Yu, X.H. / Lindqvist, Y. / Raugei, S. / Shanklin, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pp7.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pp7.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pp7_validation.pdf.gz | 724.2 KB | Display | wwPDB validaton report |
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Full document | 7pp7_full_validation.pdf.gz | 728 KB | Display | |
Data in XML | 7pp7_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 7pp7_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/7pp7 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/7pp7 | HTTPS FTP |
-Related structure data
Related structure data | 2uw1S 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
#1: Protein | Mass: 39453.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The construct used for crystallisation was an N- terminal truncation mutant (N-delta11 construct) relative to the c-DNA sequence lacking the chloroplast transit peptide. i.e. removal of: mastithppplk Source: (gene. exp.) Thunbergia alata (black-eyed Susan vine) Plasmid: pET9d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold References: UniProt: Q41510, acyl-[acyl-carrier-protein] 6-desaturase | ||||
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#2: Chemical | #3: 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: 2.02 Å3/Da / Density % sol: 39.16 % / Description: Irregular shaped crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.25M CaCl2, 0.1M Tris pH 8.0 and 16% PEG 6000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→55.59 Å / Num. obs: 19684 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.135 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2 / Num. unique obs: 1509 / CC1/2: 0.622 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2uw1 Resolution: 2.05→55.59 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.861 / SU B: 6.33 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 119.75 Å2 / Biso mean: 26.306 Å2 / Biso min: 9.19 Å2
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Refinement step | Cycle: final / Resolution: 2.05→55.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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