+Open data
-Basic information
Entry | Database: PDB / ID: 2hys | ||||||
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Title | Crystal structure of nitrophorin 2 complexed with cyanide | ||||||
Components | Nitrophorin-2 | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / cyanide | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å | ||||||
Authors | Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2007 Title: Assignment of the Ferriheme Resonances of the Low-Spin Complexes of Nitrophorins 1 and 4 by (1)H and (13)C NMR Spectroscopy: Comparison to Structural Data Obtained from X-ray Crystallography. Authors: Shokhireva, T.Kh. / Weichsel, A. / Smith, K.M. / Berry, R.E. / Shokhirev, N.V. / Balfour, C.A. / Zhang, H. / Montfort, W.R. / Walker, F.A. #1: Journal: J.Biol.Chem. / Year: 2000 Title: The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus. Authors: Andersen, J.F. / 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 | 2hys.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hys.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hys_validation.pdf.gz | 802 KB | Display | wwPDB validaton report |
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Full document | 2hys_full_validation.pdf.gz | 805.2 KB | Display | |
Data in XML | 2hys_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2hys_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/2hys ftp://data.pdbj.org/pub/pdb/validation_reports/hy/2hys | HTTPS FTP |
-Related structure data
Related structure data | 1peeS 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: 20080.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q26241 |
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#2: Chemical | ChemComp-CYN / |
#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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 89% saturated sodium citrate, 100 mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 18, 2006 / Details: bent Si-mirror |
Radiation | Monochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→22 Å / Num. all: 42640 / Num. obs: 42640 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3225 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1PEE Resolution: 1.2→22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.701 / SU ML: 0.034 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Fe-CN distance restrained to 2.0 A
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.842 Å2
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Refine analyze | Luzzati coordinate error obs: 0.182 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.23 Å / Total num. of bins used: 20
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