+Open data
-Basic information
Entry | Database: PDB / ID: 5bmg | ||||||
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Title | Nitroxide Spin Labels in Protein GB1: E15 Mutant | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | IMMUNE SYSTEM / Bacterial Proteins / Crystallization / Electron Spin Resonance Spectroscopy | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. group G (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cunningham, T.C. / Horne, W.S. / Saxena, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: Rotameric preferences of a protein spin label at edge-strand beta-sheet sites. Authors: Cunningham, T.F. / Pornsuwan, S. / Horne, W.S. / Saxena, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bmg.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bmg.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 5bmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bmg_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5bmg_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5bmg_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5bmg_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/5bmg ftp://data.pdbj.org/pub/pdb/validation_reports/bm/5bmg | HTTPS FTP |
-Related structure data
Related structure data | 5bmhC 5bmiC 2qmtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Antibody | Mass: 6202.838 Da / Num. of mol.: 8 / Fragment: UNP residues 304-357 / Mutation: E15C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909 #2: Chemical | ChemComp-MTN / #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: 2.12 Å3/Da / Density % sol: 41.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.11 Å / Num. obs: 21244 / % possible obs: 97.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.7 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QMT Resolution: 2.2→27.075 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 35.09 / Stereochemistry target values: TWIN_LSQ_F
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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: 2.2→27.075 Å
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Refine LS restraints |
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LS refinement shell |
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