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- PDB-8gtg: Corticotropin-releasing hormone receptor 1(CRF1R) bound with BMK-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gtg | ||||||
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Title | Corticotropin-releasing hormone receptor 1(CRF1R) bound with BMK-I-152 by XFEL | ||||||
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Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, H.S. / Kim, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure-based drug discovery of a corticotropin-releasing hormone receptor 1 antagonist using an X-ray free-electron laser. Authors: Kim, H. / Lim, T. / Ha, G.E. / Lee, J.Y. / Kim, J.W. / Chang, N. / Kim, S.H. / Kim, K.H. / Lee, J. / Cho, Y. / Kim, B.W. / Abrahamsson, A. / Kim, S.H. / Kim, H.J. / Park, S. / Lee, S.J. / ...Authors: Kim, H. / Lim, T. / Ha, G.E. / Lee, J.Y. / Kim, J.W. / Chang, N. / Kim, S.H. / Kim, K.H. / Lee, J. / Cho, Y. / Kim, B.W. / Abrahamsson, A. / Kim, S.H. / Kim, H.J. / Park, S. / Lee, S.J. / Park, J. / Cheong, E. / Kim, B.M. / Cho, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.7 KB | Display | ![]() |
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PDB format | ![]() | 141.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gtiC ![]() 8gtmC ![]() 4k5yS S: Starting model for refinement C: citing same article ( |
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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: 32685.355 Da / Num. of mol.: 1 Mutation: V120A, L144A, W156A, S160A, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 18113.703 Da / Num. of mol.: 1 / Mutation: C1052S, C1095S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-CW9 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.27 % |
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Crystal grow![]() | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.5 Details: 0.05M Na-Citrate(4.5), 0.06M NaCl 20~30% PEG 400(w/v) |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.75→44.11 Å / Num. obs: 15559 / % possible obs: 100 % / Redundancy: 264.7 % / Biso Wilson estimate: 81.36 Å2 / CC1/2: 0.986 / CC star: 0.767 / R split: 0.1221 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.75→2.848 Å / Redundancy: 180.9 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 1561 / CC1/2: 0.46 / CC star: 0.767 / R split: 1.1069 / % possible all: 100 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4k5y Resolution: 2.75→44.11 Å / SU ML: 0.534 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.8087 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 86.59 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→44.11 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.6934129996 Å / Origin y: 0.150232532517 Å / Origin z: 12.8240694811 Å
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Refinement TLS group | Selection details: all |