+Open data
-Basic information
Entry | Database: PDB / ID: 1eqd | ||||||
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Title | CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH CN | ||||||
Components | NITROPHORIN 4 | ||||||
Keywords | SIGNALING PROTEIN / beta barrel / lipocalin fold / ferric heme / cyanide | ||||||
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 / Resolution: 1.6 Å | ||||||
Authors | Weichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 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: Journal: Structure / Year: 1998 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: Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of a nitric oxide transport protein from a blood-sucking insect. Authors: Weichsel, A. / Andresen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eqd.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eqd.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1eqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqd ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqd | HTTPS FTP |
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-Related structure data
-Links
-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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-Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SALIVA / Source: (natural) Rhodnius prolixus (insect) / References: UniProt: Q94734 |
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#2: Chemical | ChemComp-CYN / |
#3: Chemical | ChemComp-HEV / |
#4: Chemical | ChemComp-CIT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 21, 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: 1.6→11 Å / Num. all: 32484 / Num. obs: 31409 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.65 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.16 / % possible all: 76 |
Reflection | *PLUS Num. obs: 19393 / Num. measured all: 31409 |
Reflection shell | *PLUS % possible obs: 76 % / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Resolution: 1.6→11 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→11 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.21 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |