+Open data
-Basic information
Entry | Database: PDB / ID: 7dzj | ||||||
---|---|---|---|---|---|---|---|
Title | Fabp protein before hv | ||||||
Components | Fatty acid-binding protein, liver | ||||||
Keywords | RECOMBINATION / FABP | ||||||
Function / homology | Function and homology information response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Li, H. / Yu, L.-J. / Liu, X. / Shen, J.-R. / Wang, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat.Chem. / Year: 2022 Title: Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser. Authors: Liu, X. / Liu, P. / Li, H. / Xu, Z. / Jia, L. / Xia, Y. / Yu, M. / Tang, W. / Zhu, X. / Chen, C. / Zhang, Y. / Nango, E. / Tanaka, R. / Luo, F. / Kato, K. / Nakajima, Y. / Kishi, S. / Yu, H. ...Authors: Liu, X. / Liu, P. / Li, H. / Xu, Z. / Jia, L. / Xia, Y. / Yu, M. / Tang, W. / Zhu, X. / Chen, C. / Zhang, Y. / Nango, E. / Tanaka, R. / Luo, F. / Kato, K. / Nakajima, Y. / Kishi, S. / Yu, H. / Matsubara, N. / Owada, S. / Tono, K. / Iwata, S. / Yu, L.J. / Shen, J.R. / Wang, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dzj.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dzj.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dzj_validation.pdf.gz | 867.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dzj_full_validation.pdf.gz | 871.3 KB | Display | |
Data in XML | 7dzj_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 7dzj_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dzj ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dzj | HTTPS FTP |
-Related structure data
Related structure data | 7dzeC 7dzfC 7dzgC 7dzhC 7dziC 7dzkC 7dzlC 1lkkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15635.829 Da / Num. of mol.: 2 / Mutation: C69A, L71M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / References: UniProt: P07148 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.98 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M potassium thiocyanate, pH 7.0, 30% PEG 2000 monomethyl ether |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.628→47.45 Å / Num. obs: 28327 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.013 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.63→1.72 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3195 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LKK Resolution: 1.63→19.68 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.19 Å2 / Biso mean: 32.1795 Å2 / Biso min: 17.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→19.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 13.4103 Å / Origin y: -7.8783 Å / Origin z: -20.8176 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|