+Open data
-Basic information
Entry | Database: PDB / ID: 6cne | ||||||||||||
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Title | Selenomethionine variant (V29SeM) of protein GB1 | ||||||||||||
Components | Immunoglobulin G-binding protein G | ||||||||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin G-binding protein domain B1 | ||||||||||||
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 | 6cne.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cne.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cne_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 6cne_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 6cne_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 6cne_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/6cne ftp://data.pdbj.org/pub/pdb/validation_reports/cn/6cne | HTTPS FTP |
-Related structure data
Related structure data | 6c9oC 6cheC 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: 6219.598 Da / Num. of mol.: 2 / Mutation: L5Sem 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: P06654 #2: Chemical | ChemComp-MPD / ( #3: Chemical | #4: 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: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP) PH range: 4.6-4.9 |
-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: Feb 2, 2018 |
Radiation | Monochromator: Asymmetricc curved cryst / 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→25.74 Å / Num. all: 58904 / Num. obs: 29585 / % possible obs: 96.71 % / Redundancy: 2 % / Biso Wilson estimate: 7.74 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.05208 / Rpim(I) all: 0.05208 / Rrim(I) all: 0.07366 / Net I/σ(I): 16.85 |
Reflection shell | Resolution: 1.2→1.243 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4714 / Mean I/σ(I) obs: 5.61 / Num. measured obs: 5615 / Num. unique all: 2844 / Num. unique obs: 2844 / CC1/2: 0.429 / Rpim(I) all: 0.4714 / Rrim(I) all: 0.6666 / % possible all: 94.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QMT Resolution: 1.2→25.74 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→25.74 Å
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Refine LS restraints |
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LS refinement shell |
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