+Open data
-Basic information
Entry | Database: PDB / ID: 1yjh | ||||||
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Title | Crystal Structure of Cimex Nitrophorin Ferrous NO Complex | ||||||
Components | salivary nitrophorin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / ferrous heme / nitric oxide / beta sandwich / five-coordinate iron / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information vasodilation in another organism / phosphatidylinositol dephosphorylation / nitric oxide transport / phosphatase activity / iron ion binding / heme binding / extracellular space Similarity search - Function | ||||||
Biological species | Cimex lectularius (bed bug) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Weichsel, A. / Badgandi, H. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Cimex Nitrophorin NO Complex Authors: Weichsel, A. / Badgandi, H. / Montfort, W.R. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Heme-assisted S-nitrosation of a proximal thiolate in a nitric oxide transport protein Authors: Weichsel, A. / Maes, E.M. / Andersen, J.F. / Valenzuela, J.G. / Shokhireva, T.K. / 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 | 1yjh.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjh.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjh ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjh | HTTPS FTP |
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-Related structure data
Related structure data | 1ntfS 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
#1: Protein | Mass: 31746.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cimex lectularius (bed bug) / Organ: salivary glands / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 3388165, UniProt: O76745*PLUS |
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#2: Chemical | ChemComp-NO / |
#3: Chemical | ChemComp-HEM / |
#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: 1.9 Å3/Da / Density % sol: 34.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, Li2SO4, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2004 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→37.5 Å / Num. all: 30416 / Num. obs: 30416 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2616 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1NTF Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.545 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.126 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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