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Open data
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Basic information
Entry | Database: PDB / ID: 3fll | ||||||
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Title | Crystal structure of E55Q mutant of nitrophorin 4 | ||||||
![]() | Nitrophorin-4 | ||||||
![]() | TRANSPORT PROTEIN / beta barrel / lipocalin / heme / mutant / ammonia / Iron / Metal-binding / Secreted / Vasoactive / Vasodilator | ||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Montfort, W.R. / Weichsel, A. | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.8 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.4 KB | Display | ![]() |
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Full document | ![]() | 803.4 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d2uS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NH3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.42 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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