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Open data
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Basic information
Entry | Database: PDB / ID: 1d2u | ||||||
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Title | 1.15 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS | ||||||
![]() | NITROPHORIN 4 | ||||||
![]() | TRANSPORT PROTEIN / NITRIC OXIDE TRANSPORT / FERRIC HEME / ANTIHISTAMINE / VASODILATOR / LIPOCALIN / BILAN BINDING PROTEIN | ||||||
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: 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 | ![]() | 87.8 KB | Display | ![]() |
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PDB format | ![]() | 71.7 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 | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 19.8 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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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: Chemical | ChemComp-NH3 / |
#4: 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 coordination position The heme is disordered by a rotation of 180 degrees around the CHA-Fe-CHC axis. The only evidence of this disorder is the appearence of methyl groups CMB and CMC as vinyls. These extra atoms are called CBBB and CBCB. THE LOOP CONTAINING |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.44 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.0 M AMMONIUM PHOSPHATE 10 MM TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Details: Weichsel, A., (2000) Nat. Struct. Biol., 7, 551. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8727 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→52 Å / Num. all: 49629 / Num. obs: 49629 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.26 / % possible all: 74 |
Reflection | *PLUS % possible obs: 90 % / Num. measured all: 118648 |
Reflection shell | *PLUS % possible obs: 74 % |
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Processing
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Refinement | Resolution: 1.15→52 Å / Num. parameters: 15661 / Num. restraintsaints: 18721 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: SHELXL97 REFINEMENT. FE-HEME AND FE-LIGAND DISTANCES AND ANGLES WERE UNRESTRAINED.
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Refine analyze | Num. disordered residues: 6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→52 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 52 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.13 / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.13 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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