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Yorodumi- PDB-1np1: CRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1np1 | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS PROLIXUS WITH HISTAMINE | ||||||
Components | NITROPHORIN 1 | ||||||
Keywords | NITRIC OXIDE TRANSPORT / FERRIC HEME / HISTAMINE / ANTIHISTAMINE / VASODILATOR / LIPOCALIN | ||||||
Function / homology | Function and homology information histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structures of a nitric oxide transport protein from a blood-sucking insect. Authors: Weichsel, A. / Andersen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R. #1: Journal: Biochemistry / Year: 1997 Title: Nitric Oxide Binding and Crystallization of Recombinant Nitrophorin I, a Nitric Oxide Transport Protein from the Blood-Sucking Bug Rhodnius Prolixus Authors: Andersen, J.F. / Champagne, D.E. / Weichsel, A. / Ribeiro, J.M. / Balfour, C.A. / Dress, V. / 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 | 1np1.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1np1.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1np1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1np1 ftp://data.pdbj.org/pub/pdb/validation_reports/np/1np1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.70219, -0.03969, -0.71088), Vector: |
-Components
#1: Protein | Mass: 20510.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Cell line: BL21 / Organ: SALIVARY GLAND / Plasmid: PET17B-NP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q26239 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 2.8 M AMMONIUM PHOSPHATE, 0.1 M TRIS.HCL, PH 7.5, ROOM TEMPERATURE Temp details: room temp | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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 FAST / Detector: DIFFRACTOMETER / Date: Apr 10, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28 Å / Num. obs: 25247 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.041 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2→2.14 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.153 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 71252 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.153 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→15 Å / Rfactor Rfree error: 0.011 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT CORRECTION WITH K = 0.3578, B = 93.9, BIJVOET PAIRS NOT AVERAGED AND ANOMALOUS SCATTERING FOR FE+3 INCLUDED IN THE FINAL CYCLES OF REFINEMENT.
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Displacement parameters | Biso mean: 31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.035 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.295 |