+Open data
-Basic information
Entry | Database: PDB / ID: 3nhi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the AnSt-D7L1-leukotriene C4 complex | ||||||
Components | D7 protein | ||||||
Keywords | TRANSPORT PROTEIN / All helical / odorant-binding protein / ligand-binding protein / D7 | ||||||
Function / homology | Function and homology information odorant binding / vasodilation / sensory perception of smell / toxin activity / extracellular space Similarity search - Function | ||||||
Biological species | Anopheles stephensi (Asian malaria mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å | ||||||
Authors | Andersen, J.F. / Alvarenga, P.H. / Francischetti, I.M. / Calvo, E. / Sa-Nunes, A. / Ribeiro, J.M. | ||||||
Citation | Journal: Plos Biol. / Year: 2010 Title: The function and three-dimensional structure of a thromboxane a(2)/cysteinyl leukotriene-binding protein from the saliva of a mosquito vector of the malaria parasite. Authors: Alvarenga, P.H. / Francischetti, I.M. / Calvo, E. / Sa-Nunes, A. / Ribeiro, J.M. / Andersen, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nhi.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nhi.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nhi_validation.pdf.gz | 630.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3nhi_full_validation.pdf.gz | 632 KB | Display | |
Data in XML | 3nhi_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3nhi_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/3nhi ftp://data.pdbj.org/pub/pdb/validation_reports/nh/3nhi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34452.082 Da / Num. of mol.: 1 / Fragment: UNP residues 20-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles stephensi (Asian malaria mosquito) Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)pLysS / References: UniProt: Q95NY5 |
---|---|
#2: Chemical | ChemComp-EAH / ( |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30 % PEG 3000, 0.2 M Lithium sulfate, 0.1 M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.43→50 Å / Num. all: 55648 / Num. obs: 55648 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Χ2: 1.161 / Net I/σ(I): 16.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 27.41 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→25.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.1656 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9027 / SU B: 1.973 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0657 / SU Rfree: 0.0658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 86.19 Å2 / Biso mean: 13.3111 Å2 / Biso min: 3.9 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→25.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.43→1.466 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 5.5021 Å / Origin y: 1.0883 Å / Origin z: 14.2145 Å
|