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Open data
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Basic information
Entry | Database: PDB / ID: 1xf9 | ||||||
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Title | Structure of NBD1 from murine CFTR- F508S mutant | ||||||
![]() | Cystic fibrosis transmembrane conductance regulator | ||||||
![]() | TRANSPORT PROTEIN / Cystic Fibrosis / ABC transporters / nucleotide-binding domain | ||||||
Function / homology | ![]() RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / water transport / channel-conductance-controlling ATPase ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / water transport / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / negative regulation of vascular associated smooth muscle cell apoptotic process / enamel mineralization / intracellular pH elevation / negative regulation of type B pancreatic cell development / amelogenesis / chloride channel inhibitor activity / Cargo recognition for clathrin-mediated endocytosis / ABC-family proteins mediated transport / Clathrin-mediated endocytosis / multicellular organismal-level water homeostasis / Ub-specific processing proteases / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle docking involved in exocytosis / chloride transport / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / microvillus / sodium ion transmembrane transport / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / chloride transmembrane transport / isomerase activity / response to endoplasmic reticulum stress / establishment of localization in cell / PDZ domain binding / lung development / vasodilation / recycling endosome membrane / early endosome membrane / protein-folding chaperone binding / basolateral plasma membrane / early endosome / response to xenobiotic stimulus / apical plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thibodeau, P.H. / Brautigam, C.A. / Machius, M. / Thomas, P.J. | ||||||
![]() | ![]() Title: Side chain and backbone contributions of Phe508 to CFTR folding. Authors: Thibodeau, P.H. / Brautigam, C.A. / Machius, M. / Thomas, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.9 KB | Display | ![]() |
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PDB format | ![]() | 180.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 41.7 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xfaC ![]() 1r0xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 31708.928 Da / Num. of mol.: 4 / Fragment: NBD1 / Mutation: F508S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-ACY / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 4, 2004 |
Radiation | Monochromator: Double-crystal monochromator, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40.4 Å / Num. all: 44242 / Num. obs: 44242 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rsym value: 0.078 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2104 / Rsym value: 0.481 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R0X, heterogens removed Resolution: 2.7→40.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 198135.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues with electron density for the main chain but not for the side chain were included with the side-chain occupancies set to 0.00. Hydration around some Mg2+ atoms is incomplete because ...Details: Residues with electron density for the main chain but not for the side chain were included with the side-chain occupancies set to 0.00. Hydration around some Mg2+ atoms is incomplete because of lack of electron density for the waters.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2184 Å2 / ksol: 0.365999 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→40.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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