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Open data
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Basic information
Entry | Database: PDB / ID: 1ml7 | ||||||
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Title | Crystal structure of nitrophorin 4 complexed with 4-iodopyrazole | ||||||
![]() | nitrophorin 4 | ||||||
![]() | LIGAND BINDING PROTEIN / NO carrier / ferric heme / iodopyrazole / lipocalin / beta barrel / conformational change | ||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Berry, R.E. / Ding, X.D. / Weichsel, A. / Montfort, W.R. / Walker, F.A. | ||||||
![]() | ![]() Title: Axial ligand complexes of the Rhodnius nitrophorins: reduction potentials, binding constants, EPR spectra, and structures of the 4-iodopyrazole and imidazole complexes of NP4 Authors: Berry, R.E. / Ding, X.D. / Shokhireva, T.K. / Weichsel, A. / Montfort, W.R. / Walker, F.A. #1: ![]() Title: Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitophorin 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 | ![]() | 92.6 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ikjS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-HEV / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.99 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2002 |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→22 Å / Num. all: 42458 / Num. obs: 42458 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 7.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 7.2 / Num. unique all: 3947 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 21 Å / % possible obs: 98 % / Num. measured all: 219394 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.16 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1IKJ Resolution: 1.25→20.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 12.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→20.4 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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