+Open data
-Basic information
Entry | Database: PDB / ID: 1si6 | ||||||
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Title | Crystal structure of cimex nitrophorin complex with CO | ||||||
Components | salivary nitrophorin | ||||||
Keywords | TRANSPORT PROTEIN / ferrous heme / carbon monoxide / beta sandwich | ||||||
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: 1.45 Å | ||||||
Authors | Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Structure of cimex nitrophorin complex with carbon monoxide Authors: Weichsel, A. / Montfort, W.R. #1: Journal: To be Published Title: Structure of cimex nitrophorin and its complex with NO Authors: Weichsel, A. / Maes, E.A. / 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 | 1si6.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1si6.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 1si6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1si6 ftp://data.pdbj.org/pub/pdb/validation_reports/si/1si6 | 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) / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O76745 |
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#2: Chemical | ChemComp-CMO / |
#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: 2.09 Å3/Da / Density % sol: 41.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG 4000, Li2SO4, ethanol, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2003 / Details: bent Si-mirror |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→15 Å / Num. all: 44739 / Num. obs: 44739 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4654 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1NTF Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.446 / SU ML: 0.056 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CO LIGAND PARTIALLY DISORDERED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.303 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Total num. of bins used: 20
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