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- PDB-1x8n: 1.08 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1x8n | ||||||
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Title | 1.08 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 7.4 | ||||||
![]() | Nitrophorin 4 | ||||||
![]() | LIGAND BINDING PROTEIN / Lipocalin / beta barrel / heme / nitric oxide | ||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kondrashov, D.A. / Roberts, S.A. / Weichsel, A. / Montfort, W.R. | ||||||
![]() | ![]() Title: Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding Authors: Kondrashov, D.A. / Roberts, S.A. / Weichsel, 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 | ![]() | 104.7 KB | Display | ![]() |
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PDB format | ![]() | 78.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.6 KB | Display | ![]() |
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Full document | ![]() | 794.1 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1x8oC ![]() 1x8pC ![]() 1x8qC ![]() 1koiS 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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Details | The biological assembly is a monomer consisting of chain A and the heme, and can be generated by the identity operation: x,y,z |
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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-HEM / |
#3: Chemical | ChemComp-NO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 24.7 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: ammonium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2002 / Details: Flat mirror (vertical focusing) |
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→36 Å / Num. all: 66157 / Num. obs: 66157 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.08→1.12 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6226 / Rsym value: 0.27 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KOI Resolution: 1.08→6 Å / Num. parameters: 16428 / Num. restraintsaints: 15840 Isotropic thermal model: anisotropic, except for residues 32-26 and 126-130 Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.6%. Addition of hydrogens in calculated positions further reduced free R by 1.3%
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Displacement parameters | Biso mean: 14.3 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.133 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 60 / Occupancy sum hydrogen: 1341 / Occupancy sum non hydrogen: 1766.55 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→6 Å
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Refine LS restraints |
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