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- PDB-6cpz: Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cpz | ||||||||||||
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Title | Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction | ||||||||||||
![]() | Immunoglobulin G-binding protein G | ||||||||||||
![]() | IMMUNE SYSTEM / Immunoglobulin G-binding protein domain B1 | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chen, Q. / Rozovsky, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 77Se NMR Probes the Protein Environment of Selenomethionine. Authors: Chen, Q. / Xu, S. / Lu, X. / Boeri, M.V. / Pepelyayeva, Y. / Diaz, E.L. / Soni, S.D. / Allaire, M. / Forstner, M.B. / Bahnson, B.J. / Rozovsky, 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 | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.1 KB | Display | ![]() |
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Full document | ![]() | 468.1 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c9oC ![]() 6cheC ![]() 6cneC ![]() 6cteC ![]() 2qmtS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 6219.598 Da / Num. of mol.: 2 / Mutation: I6Sem Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 48% MPD 20% IPA 25 mM sodium acetate buffer pH 4.7 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP PH range: 4.5-4.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2017 |
Radiation | Monochromator: Asymetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→27.571 Å / Num. obs: 69779 / % possible obs: 97.43 % / Redundancy: 2 % / Biso Wilson estimate: 7.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01784 / Rpim(I) all: 0.01784 / Rrim(I) all: 0.02524 / Net I/σ(I): 12.98 |
Reflection shell | Resolution: 1.12→1.16 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QMT Resolution: 1.12→27.571 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.1 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→27.571 Å
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Refine LS restraints |
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LS refinement shell |
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