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Open data
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Basic information
Entry | Database: PDB / ID: 7dzf | ||||||
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Title | Intermediate of FABP with a delay time of 10 ns | ||||||
![]() | Fatty acid-binding protein, liver | ||||||
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Function / homology | ![]() response to vitamin B3 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Yu, L.-J. / Liu, X. / Shen, J.-R. / Wang, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.3 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dzeC ![]() 7dzgC ![]() 7dzhC ![]() 7dziC ![]() 7dzjC ![]() 7dzkC ![]() 7dzlC ![]() 1lkkS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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