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Yorodumi- PDB-6c9o: Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c9o | ||||||||||||
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Title | Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction | ||||||||||||
Components | Immunoglobulin G-binding protein G | ||||||||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin G-binding protein G protein | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptococcus sp. group G (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||||||||
Authors | Chen, Q. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Phys.Chem.B / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c9o.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c9o.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 6c9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9o ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9o | HTTPS FTP |
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-Related structure data
Related structure data | 6cheC 6cneC 6cpzC 6cteC 2qmtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: Antibody | Mass: 6233.625 Da / Num. of mol.: 2 / Mutation: V29M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Cell line (production host): BL21DE3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909 #2: Chemical | ChemComp-MPD / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.11 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 46% MPD, 20% IPA, 25 mM sodium acetate pH 4.5 / PH range: 4.5-4.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2017 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→29.1 Å / Num. obs: 29169 / % possible obs: 97.03 % / Redundancy: 2 % / Biso Wilson estimate: 9.47 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.02561 / Rpim(I) all: 0.02561 / Rrim(I) all: 0.03622 / Net I/σ(I): 9.36 |
Reflection shell | Resolution: 1.2→1.243 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1201 / Num. unique obs: 2768 / CC1/2: 0.979 / Rpim(I) all: 0.1201 / Rrim(I) all: 0.1698 / % possible all: 93.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QMT Resolution: 1.2→29.099 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9 / 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: 1.2→29.099 Å
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Refine LS restraints |
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LS refinement shell |
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