+Open data
-Basic information
Entry | Database: PDB / ID: 1np4 | ||||||
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Title | CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS | ||||||
Components | PROTEIN (NITROPHORIN 4) | ||||||
Keywords | TRANSPORT PROTEIN / NITRIC OXIDE TRANSPORT / FERRIC HEME / ANTIHISTAMINE / VASODILATOR / LIPOCALIN / BILIN BINDING PROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Andersen, J.F. / Weichsel, A. / Champagne, D.E. / Balfour, C.A. / Montfort, W.R. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1np4.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1np4.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 1np4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1np4_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 1np4_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 1np4_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1np4_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1np4 ftp://data.pdbj.org/pub/pdb/validation_reports/np/1np4 | HTTPS FTP |
-Related structure data
Related structure data | 1np1S S: Starting model for refinement |
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Similar 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 genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Organ: SALIVARY GLAND / Plasmid: PET17B-NP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q94734 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NH3 / |
#4: 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: 2.01 Å3/Da / Density % sol: 38.79 % | |||||||||||||||
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Crystal grow | pH: 5.6 Details: 2.8 M AMMONIUM PHOSPHATE, 0.1 M NA CACODYLATE, PH 5.6 (FINAL PH 7.5), ROOM TEMPERATURE Temp details: room temp | |||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used to seeding | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Oct 22, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22 Å / Num. obs: 23988 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 18.66 Å2 / Rsym value: 0.039 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.135 / % possible all: 74.1 |
Reflection | *PLUS Num. measured all: 49805 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 74.1 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NP1 Resolution: 1.5→21 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 21 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.275 / Rfactor Rwork: 0.28 |