+Open data
-Basic information
Entry | Database: PDB / ID: 1afr | ||||||
---|---|---|---|---|---|---|---|
Title | STEAROYL-ACYL CARRIER PROTEIN DESATURASE FROM CASTOR SEEDS | ||||||
Components | DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID DESATURASE / FATTY ACID BIOSYNTHESIS / BINUCLEAR IRON CENTER / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information stearoyl-[acyl-carrier-protein] 9-desaturase / : / stearoyl-[ACP] desaturase activity / stearoyl-CoA 9-desaturase activity / chloroplast stroma / fatty acid biosynthetic process / defense response / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Ricinus communis (castor bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR, NCS / Resolution: 2.4 Å | ||||||
Authors | Lindqvist, Y. / Huang, W. / Schneider, G. | ||||||
Citation | Journal: EMBO J. / Year: 1996 Title: Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. Authors: Lindqvist, Y. / Huang, W. / Schneider, G. / Shanklin, J. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Preliminary Crystallographic Data for Stearoyl-Acyl Carrier Protein Desaturase from Castor Seed Authors: Schneider, G. / Lindqvist, Y. / Shanklin, J. / Somerville, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1afr.cif.gz | 427.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1afr.ent.gz | 351.2 KB | Display | PDB format |
PDBx/mmJSON format | 1afr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1afr_validation.pdf.gz | 392.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1afr_full_validation.pdf.gz | 421.6 KB | Display | |
Data in XML | 1afr_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 1afr_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1afr ftp://data.pdbj.org/pub/pdb/validation_reports/af/1afr | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 39754.074 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Tissue: SEEDS / Organ: SEED / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P22337, EC: 1.14.99.6 #2: Chemical | ChemComp-FE2 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 79674 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 |
Reflection | *PLUS Num. measured all: 403539 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR, NCS / Resolution: 2.4→7 Å / Isotropic thermal model: RESTRAINED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |