+Open data
-Basic information
Entry | Database: PDB / ID: 6lcq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of rice defensin OsAFP1 | |||||||||
Components | Defensin-like protein CAL1 | |||||||||
Keywords | ANTIFUNGAL PROTEIN / Rice / Oryza sativa / Defensin / Antifungal / Cysteine-stabilized alpha/beta structure | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Oryza sativa (Asian cultivated rice) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | |||||||||
Authors | Ochiai, A. / Ogawa, K. / Fukuda, M. / Suzuki, M. / Ito, K. / Tanaka, T. / Sagehashi, Y. / Taniguchi, M. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: J.Biosci.Bioeng. / Year: 2020 Title: Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding. Authors: Ochiai, A. / Ogawa, K. / Fukuda, M. / Suzuki, M. / Ito, K. / Tanaka, T. / Sagehashi, Y. / Taniguchi, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6lcq.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6lcq.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lcq ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lcq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2lr3S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 5975.935 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) Gene: CAL1, CPT1, PR12, Os02g0629800, LOC_Os02g41904, B1469H02.30, OsJ_07607 Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) pLysS / References: UniProt: Q6K209 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 20% w/v polyethylene glycol 3350, 0.1 M potassium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 12570 / % possible obs: 99.7 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 12570 / % possible all: 96.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LR3 Resolution: 1.62→19.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.789 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.17 Å2 / Biso mean: 19.021 Å2 / Biso min: 5.98 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.62→19.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.62→1.65 Å / Rfactor Rfree error: 0
|