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Yorodumi- PDB-7fcx: Room temperature structure of the human heart fatty acid-binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fcx | |||||||||||||||
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Title | Room temperature structure of the human heart fatty acid-binding protein complexed with hexanoic acid | |||||||||||||||
Components | Fatty acid-binding protein, heart | |||||||||||||||
Keywords | LIPID BINDING PROTEIN / FABP / Complex / Binding protein / hexanoic acid | |||||||||||||||
Function / homology | Function and homology information positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||||||||
Authors | Sugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: To Be Published Title: Room temperature structure of the human heart fatty acid-binding protein complexed with hexanoic acid Authors: Sugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fcx.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fcx.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 7fcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/7fcx ftp://data.pdbj.org/pub/pdb/validation_reports/fc/7fcx | HTTPS FTP |
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-Related structure data
Related structure data | 4tjzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14879.022 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413 |
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#2: Chemical | ChemComp-6NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl (pH8.5), 50% PEG 400 |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. obs: 48996 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rpim(I) all: 0.037 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.15→1.17 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2303 / Rpim(I) all: 0.311 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TJZ Resolution: 1.15→29.91 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.971 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.041 / 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: 16.895 Å2
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Refinement step | Cycle: 1 / Resolution: 1.15→29.91 Å
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Refine LS restraints |
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