+Open data
-Basic information
Entry | Database: PDB / ID: 7dzf | ||||||
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Title | Intermediate of FABP with a delay time of 10 ns | ||||||
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Li, H. / Yu, L.-J. / Liu, X. / Shen, J.-R. / Wang, J. | ||||||
Funding support | China, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dzf.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dzf.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dzf_validation.pdf.gz | 930.1 KB | Display | wwPDB validaton report |
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Full document | 7dzf_full_validation.pdf.gz | 921 KB | Display | |
Data in XML | 7dzf_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7dzf_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dzf ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dzf | HTTPS FTP |
-Related structure data
Related structure data | 7dzeC 7dzgC 7dzhC 7dziC 7dzjC 7dzkC 7dzlC 1lkkS C: citing same article (ref.) 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: 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 | |
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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: 2.07 Å3/Da / Density % sol: 40.58 % |
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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: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 30937 / % possible obs: 100 % / Redundancy: 84 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.98 / Net I/σ(I): 85 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 58 % / Num. unique obs: 3060 / CC1/2: 0.39 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LKK Resolution: 1.7→19.91 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.31 Å2 / Biso mean: 31.6808 Å2 / Biso min: 12.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→19.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 13.8362 Å / Origin y: -7.9728 Å / Origin z: -21.2753 Å
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Refinement TLS group |
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