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Yorodumi- PDB-7fz2: Crystal Structure of human FABP4 in complex with [3-oxo-5-[4-(tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fz2 | ||||||
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Title | Crystal Structure of human FABP4 in complex with [3-oxo-5-[4-(trifluoromethyl)phenyl]cyclohexen-1-yl] acetate | ||||||
Components | Fatty acid-binding protein, adipocyte | ||||||
Keywords | LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING | ||||||
Function / homology | Function and homology information hormone receptor binding / white fat cell differentiation / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / long-chain fatty acid transport / Triglyceride catabolism / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / white fat cell differentiation / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / long-chain fatty acid transport / Triglyceride catabolism / fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Ehler, A. / Benz, J. / Obst, U. / Kumagai, Y. / Rudolph, M.G. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To be published Title: Crystal Structure of a human FABP4 complex Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fz2.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fz2.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 7fz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fz2_validation.pdf.gz | 1022.7 KB | Display | wwPDB validaton report |
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Full document | 7fz2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7fz2_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 7fz2_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/7fz2 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/7fz2 | HTTPS FTP |
-Group deposition
ID | G_1002264 (222 entries) |
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Title | To be published |
Type | undefined |
Description | A set of fabp crystal structures |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15022.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090 |
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-Non-polymers , 5 types, 190 molecules
#2: Chemical | ChemComp-WDI / ( | ||||||
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#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.12→37.59 Å / Num. obs: 50917 / % possible obs: 99.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 15.962 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.037 / Rsym value: 0.037 / Χ2: 0.919 / Net I/σ(I): 18.58 / Num. measured all: 309610 / Scaling rejects: 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 1.12→37.58 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.828 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: starting material was chiral, hydrolysis product is achiral two conformations with different pucker of cyclohexenyl ring and different rotation of trifluoromethyl group present
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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 max: 60.88 Å2 / Biso mean: 16.253 Å2 / Biso min: 7.43 Å2
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Refinement step | Cycle: final / Resolution: 1.12→37.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.123→1.152 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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