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- PDB-1koi: CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEX... -
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Basic information
Entry | Database: PDB / ID: 1koi | |||||||||
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Title | CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEXED WITH NITRIC OXIDE AT 1.08 A RESOLUTION | |||||||||
![]() | NITROPHORIN 4 | |||||||||
![]() | TRANSPORT PROTEIN / nitric oxide transport / ferric heme / anithistimine / lipocalin | |||||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Roberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.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 | ![]() | 99.3 KB | Display | ![]() |
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PDB format | ![]() | 74.3 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 | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d2uC ![]() 1ikeC ![]() 1ikjC ![]() 1erxS S: Starting model for refinement C: citing same article ( |
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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: 20292.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NITRIC OXIDE OCCUPIES THE SIXTH COORDINATION POSITION OF THE IRON. THE HEME IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. THE ONLY EVIDENCE OF THIS DISORDER IS THE ...Details: NITRIC OXIDE OCCUPIES THE SIXTH COORDINATION POSITION OF THE IRON. THE HEME IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. THE ONLY EVIDENCE OF THIS DISORDER IS THE APPEARANCE OF METHYL GROUPS CMB AND CMC AS VINYLS. THESE EXTRA ATOMS ARE CALLED CBBB AND CBCB. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO / |
#4: Water | ChemComp-HOH / |
-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: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1→30 Å / Num. all: 83813 / Num. obs: 62726 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 4.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 38 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 15 / % possible all: 70 |
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Processing
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Refinement | Starting model: pdb entry 1ERX Resolution: 1.08→30 Å / Isotropic thermal model: All non-hydrogen atoms anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Shelx conjugate gradient refinement. Hydrogen atoms added at calculated positions. Heme and iron coordination sphere refined without restraints.
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Displacement parameters | Biso mean: 13 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→30 Å
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