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- PDB-1d3s: 1.4 A crystal structure of nitrophorin 4 from Rhodnius prolixis a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d3s | ||||||
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Title | 1.4 A crystal structure of nitrophorin 4 from Rhodnius prolixis at pH=5.6. | ||||||
![]() | NITROPHORIN 4 | ||||||
![]() | TRANSPORT PROTEIN / NITRIC OXIDE TRANSPORT / FERRIC HEME / ANTIHISTAMINE / VASODILATOR / LIPOCALIN | ||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Weichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R. | ||||||
![]() | ![]() Title: Nitric oxide binding to nitrophorin 4 induces complete distal pocket burial. Authors: Weichsel, A. / Andersen, J.F. / Roberts, S.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 | ![]() | 51.9 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | AMMONIA (NH3) OCCUPIES THE FE SIXTH COORDINATION POSITION. THE HEME IS DISORDERED BY A ROTATION OF ...AMMONIA (NH3) OCCUPIES THE FE SIXTH COORDINATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.51 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 23% PEG 4000 20 MM SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 25227 / Num. obs: 25227 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.65 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / % possible all: 79 |
Reflection | *PLUS Num. measured all: 66833 |
Reflection shell | *PLUS % possible obs: 79 % |
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Processing
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Refinement | Resolution: 1.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH-HUBER Details: SHELXL REFINEMENT, FE, S ATOMS ANISOTROPIC (EXCEPT FOR C41SG WHICH IS DISORDERED) FE-LIGAND DISTANCES/ANGLES NOT RESTRAINED.
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.2 / Rfactor obs: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |