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Yorodumi- PDB-4l21: Crystal structure of Cimex nitrophorin F64V mutant ferrous NO complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l21 | ||||||
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Title | Crystal structure of Cimex nitrophorin F64V mutant ferrous NO complex | ||||||
Components | Salivary nitrophorin | ||||||
Keywords | TRANSPORT PROTEIN / beta sandwich / ferrous heme / thiolate heme ligand / s-nitrosocysteine | ||||||
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 | Badgandi, H.B. / Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Proximal Cysteine Protonation in Cimex Nitrophorin is key to efficient NO transport and release. Authors: Badgandi, H.B. / Hazzard, J.T. / Weichsel, A. / Tollin, G. / 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 | 4l21.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l21.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 4l21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/4l21 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/4l21 | HTTPS FTP |
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-Related structure data
Related structure data | 4l1yC 4l1zC 4l20C 1ntfS S: Starting model for refinement C: citing same article (ref.) |
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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: 31583.299 Da / Num. of mol.: 1 / Fragment: unp residues 23-302 / Mutation: F64V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cimex lectularius (bed bug) / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O76745 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO / |
#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: 2.12 Å3/Da / Density % sol: 41.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, pH 5.6, 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: 0.9798 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 23, 2008 / 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: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→21.74 Å / Num. all: 176907 / Num. obs: 32033 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.52 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5.44 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3166 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1NTF Resolution: 1.65→21.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.115 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.106 / 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: 27.612 Å2
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Refine analyze | Luzzati coordinate error obs: 0.211 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→21.74 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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