+Open data
-Basic information
Entry | Database: PDB / ID: 3mp9 | ||||||
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Title | Structure of Streptococcal protein G B1 domain at pH 3.0 | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | PROTEIN BINDING / PROTEIN G / IGG-BINDING 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 | Tomlinson, J.H. / Green, V.L. / Baker, P.J. / Williamson, M.P. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structural origins of pH-dependent chemical shifts in the B1 domain of protein G. Authors: Tomlinson, J.H. / Green, V.L. / Baker, P.J. / Williamson, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mp9.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mp9.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mp9 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mp9 | HTTPS FTP |
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-Related structure data
Related structure data | 1pgaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 7216.829 Da / Num. of mol.: 2 / Fragment: B1 domain (UNP residues 227-282) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P06654 #2: Chemical | #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: 1.74 Å3/Da / Density % sol: 29.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 3 Details: Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, ...Details: Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2009 / Details: mirrors |
Radiation | Monochromator: dual crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30.15 Å / Num. all: 29246 / Num. obs: 27757 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3333 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PGA Resolution: 1.2→30.15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.34 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→30.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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