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Open data
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Basic information
Entry | Database: PDB / ID: 8gdy | ||||||
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Title | Crystal structure of the human PDI first domain with 9 mutations | ||||||
![]() | Protein disulfide-isomerase![]() | ||||||
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Function / homology | ![]() regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / interleukin-23-mediated signaling pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Banayan, N.E. / Loughlin, B.L. / Singh, S. / Wong, V. / Hunt, H.S. / Handelman, S.K. / Price, N. / Hunt, J.F. | ||||||
Funding support | 1items
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![]() | ![]() Title: Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution. Authors: Banayan, N.E. / Loughlin, B.J. / Singh, S. / Forouhar, F. / Lu, G. / Wong, K.H. / Neky, M. / Hunt, H.S. / Bateman Jr., L.B. / Tamez, A. / Handelman, S.K. / Price, W.N. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gduC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 15831.599 Da / Num. of mol.: 2 Mutation: K31R, K42R, K57R, K65R, K69R, K71R, K114R, K130R, K131R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-EDO / | ![]() #4: 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: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow![]() | Temperature: 277 K / Method: microbatch / pH: 6 Details: 0.1 M potassium thiocyanate, 0.1 M MES, and 24% (w/v) PEG 20k |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.89→68.56 Å / Num. obs: 20332 / % possible obs: 98.8 % / Redundancy: 12.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.238 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.148 / Num. unique obs: 1062 / CC1/2: 0.457 / % possible all: 82.2 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→45.7 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: -15.3877 Å / Origin y: -15.1971 Å / Origin z: 16.9988 Å
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Refinement TLS group | Selection details: all |