[English] 日本語
Yorodumi- PDB-2j2f: The T199D Mutant of Stearoyl Acyl Carrier Protein Desaturase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j2f | ||||||
---|---|---|---|---|---|---|---|
Title | The T199D Mutant of Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean) | ||||||
Components | ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSFER / FOUR-HELIX BUNDLE / LIPID SYNTHESIS / TRANSIT PEPTIDE / FATTY ACID BIOSYNTHESIS / NADP / CHLOROPLAST / DI-RON ENZYME | ||||||
Function / homology | Function and homology information stearoyl-[acyl-carrier-protein] 9-desaturase / : / stearoyl-[ACP] desaturase activity / stearoyl-CoA 9-desaturase activity / chloroplast stroma / defense response / fatty acid biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | RICINUS COMMUNIS (castor bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Guy, J.E. / Abreu, I.A. / Moche, M. / Lindqvist, Y. / Whittle, E. / Shanklin, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: A Single Mutation in the Castor {Delta}9-18:0- Desaturase Changes Reaction Partitioning from Desaturation to Oxidase Chemistry. Authors: Guy, J.E. / Abreu, I.A. / Moche, M. / Lindqvist, Y. / Whittle, E. / Shanklin, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2j2f.cif.gz | 404.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2j2f.ent.gz | 331.7 KB | Display | PDB format |
PDBx/mmJSON format | 2j2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j2f_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2j2f_full_validation.pdf.gz | 549.3 KB | Display | |
Data in XML | 2j2f_validation.xml.gz | 74.2 KB | Display | |
Data in CIF | 2j2f_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/2j2f ftp://data.pdbj.org/pub/pdb/validation_reports/j2/2j2f | HTTPS FTP |
-Related structure data
Related structure data | 1afrS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
|
-Components
#1: Protein | Mass: 41717.297 Da / Num. of mol.: 6 / Fragment: RESIDUES 34-396 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RICINUS COMMUNIS (castor bean) / Plasmid: PET9D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22337, EC: 1.14.99.6 #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 232 TO ASP ...ENGINEERED | Sequence details | MUTANT - T199D | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.77 % |
---|---|
Crystal grow | pH: 5.4 Details: 0.08M CACODYLATE PH 5.4 0.2M MAGNESIUM ACETATE 75MM AMMONIUM SULFATE 16-18% PEG 4000 0.2% BOG |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→40 Å / Num. obs: 68082 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFR Resolution: 2.65→40 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 31.663 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|