[English] 日本語
Yorodumi- PDB-1koi: CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1koi | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEXED WITH NITRIC OXIDE AT 1.08 A RESOLUTION | |||||||||
Components | NITROPHORIN 4 | |||||||||
Keywords | TRANSPORT PROTEIN / nitric oxide transport / ferric heme / anithistimine / lipocalin | |||||||||
Function / homology | Function and homology information nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodnius prolixus (insect) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.08 Å | |||||||||
Authors | Roberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1koi.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1koi.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1koi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1koi ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1koi | HTTPS FTP |
---|
-Related structure data
Related structure data | 1d2uC 1ikeC 1ikjC 1erxS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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.) Rhodnius prolixus (insect) / Plasmid: PET-17B-NP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q94734 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.44 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.975 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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.
| ||||||||||||||||||||
Displacement parameters | Biso mean: 13 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→30 Å
|