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Open data
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Basic information
Entry | Database: PDB / ID: 7mxf | ||||||
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Title | CD1c with antigen analogue 2 | ||||||
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![]() | LIPID BINDING PROTEIN / ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, T.P. / Shahine, A. / Rossjohn, J. | ||||||
![]() | ![]() Title: Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells. Authors: Reijneveld, J.F. / Marino, L. / Cao, T.P. / Cheng, T.Y. / Dam, D. / Shahine, A. / Witte, M.D. / Filippov, D.V. / Suliman, S. / van der Marel, G.A. / Moody, D.B. / Minnaard, A.J. / Rossjohn, ...Authors: Reijneveld, J.F. / Marino, L. / Cao, T.P. / Cheng, T.Y. / Dam, D. / Shahine, A. / Witte, M.D. / Filippov, D.V. / Suliman, S. / van der Marel, G.A. / Moody, D.B. / Minnaard, A.J. / Rossjohn, J. / Codee, J.D.C. / Van Rhijn, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.2 KB | Display | ![]() |
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PDB format | ![]() | 139.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7mx4SC ![]() 7mxhC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31998.793 Da / Num. of mol.: 1 / Mutation: N52Q, N57Q, K108G, N128Q, Y242G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 12616.132 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / ![]() |
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-Non-polymers , 6 types, 142 molecules ![](data/chem/img/NHE.gif)
![](data/chem/img/ZQ4.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/ZP7.gif)
![](data/chem/img/MLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZQ4.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/ZP7.gif)
![](data/chem/img/MLA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NHE / ![]() |
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#5: Chemical | ChemComp-ZQ4 / |
#6: Chemical | ChemComp-D12 / ![]() |
#7: Chemical | ChemComp-ZP7 / ( |
#8: Chemical | ChemComp-MLA / ![]() |
#9: Water | ChemComp-HOH / ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 100 mM CHES, 1.05 M sodium citrate, 25 mM triglycine |
-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: Oct 9, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→43.67 Å / Num. obs: 27417 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 33.15 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02746 / Rpim(I) all: 0.02746 / Rrim(I) all: 0.03883 / Net I/σ(I): 12.26 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3289 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 2711 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.3289 / Rrim(I) all: 0.4651 / % possible all: 99.96 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 7MX4 Resolution: 2→43.67 Å / SU ML: 0.2224 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4862 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: 39.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.67 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: -13.5939469441 Å / Origin y: -17.8764475509 Å / Origin z: 16.728618256 Å
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Refinement TLS group | Selection details: all |