+Open data
-Basic information
Entry | Database: PDB / ID: 3fll | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E55Q mutant of nitrophorin 4 | ||||||
Components | Nitrophorin-4 | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / lipocalin / heme / mutant / ammonia / Iron / Metal-binding / Secreted / Vasoactive / Vasodilator | ||||||
Function / homology | Function and homology information nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Montfort, W.R. / Weichsel, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes. Authors: Berry, R.E. / Shokhirev, M.N. / Ho, A.Y. / Yang, F. / Shokhireva, T.K. / Zhang, H. / Weichsel, A. / Montfort, W.R. / Walker, F.A. #1: Journal: Biochemistry / Year: 2001 Title: Ligand-induced heme ruffling and bent NO geometry in ultra-high-resolution structures of nitrophorin 4 Authors: Roberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fll.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fll.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/3fll ftp://data.pdbj.org/pub/pdb/validation_reports/fl/3fll | HTTPS FTP |
---|
-Related structure data
Related structure data | 1d2uS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20291.678 Da / Num. of mol.: 1 / Fragment: UNP residues 22-205 / Mutation: E55Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q94734 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NH3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.42 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.751 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2008 / Details: mirrors |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.751 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.6 Å / Num. obs: 23089 / % possible obs: 95.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2527 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1D2U Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.353 / SU ML: 0.052 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.663 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
|