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Yorodumi- PDB-3akm: X-ray structure of iFABP from human and rat with bound fluorescen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3akm | ||||||
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Title | X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue | ||||||
Components | Fatty acid-binding protein, intestinal | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / ligand complex / fatty acid binding protein | ||||||
Function / homology | Function and homology information intestinal lipid absorption / apical cortex / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / microvillus / fatty acid transport / fatty acid metabolic process / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wielens, J. / Laguerre, A.J.K. / Parker, M.W. / Scanlon, M.J. | ||||||
Citation | Journal: To be Published Title: Crystal structures of human and rat intestinal fatty acid binding proteins in complex with 11-(Dansylamino)undecanoic acid Authors: Laguerre, A.J.K. / Wielens, J. / Parker, M.W. / Porter, C.J. / Scanlon, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3akm.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3akm.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 3akm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3akm ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3akm | HTTPS FTP |
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-Related structure data
Related structure data | 3ifbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15098.044 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12104 #2: Chemical | ChemComp-11D / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30-34% w/v PEG 4000, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2008 / Details: mirrors |
Radiation | Monochromator: silicon 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50.8 Å / Num. all: 39532 / Num. obs: 39319 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.12 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5728 / Rsym value: 0.57 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IFB Resolution: 1.9→33.48 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 52.53 Å2 / Biso mean: 21.477 Å2 / Biso min: 7.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→33.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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