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Open data
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Basic information
Entry | Database: PDB / ID: 1erx | ||||||
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Title | CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH NO | ||||||
![]() | NITROPHORIN 4 | ||||||
![]() | SIGNALING PROTEIN / beta barrel / ferric heme / nitric oxide complex | ||||||
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. #1: ![]() Title: The crystal structure of nitrophorin 4 at 1.5 A resolution: transport of nitric oxide by a lipocalin-based heme protein. Authors: Andersen, J.F. / Weichsel, A. / Balfour, C.A. / Champagne, D.E. / Montfort, W.R. #2: ![]() Title: Nitric oxide binding to the ferri- and ferroheme states of nitrophorin 1, a reversible NO-binding heme protein from the saliva of the blood-sucking insect, rhodnius prolixus. Authors: Ding, X.D. / Weichsel, A. / Andersen, J.F. / Shokhireva, T.K. / Balfour, C.A. / Pierik, A.J. / Averill, B.A. / Montfort, W.R. / Walker, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.4 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.3 KB | Display | ![]() |
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Full document | ![]() | 500.2 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 9.9 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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Details | biological assembly is a monomer |
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Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SALIVA / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-HEV / |
#3: Chemical | ChemComp-NO / |
#4: Chemical | ChemComp-CIT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.48 % | ||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of 1:1 mixture of well and protein solutions | ||||||||||||||||||||||||||||||
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: Apr 29, 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→15 Å / Num. all: 28023 / Num. obs: 28023 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3 / Num. unique all: 3546 / % possible all: 79 |
Reflection | *PLUS Num. measured all: 56842 |
Reflection shell | *PLUS % possible obs: 79 % / Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Resolution: 1.4→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: anisotropic temperature factor refinement
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Refinement step | Cycle: LAST / Resolution: 1.4→15 Å
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Refine LS restraints |
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