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Open data
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Basic information
Entry | Database: PDB / ID: 3mp9 | ||||||
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Title | Structure of Streptococcal protein G B1 domain at pH 3.0 | ||||||
![]() | Immunoglobulin G-binding protein G | ||||||
![]() | PROTEIN BINDING / PROTEIN G / IGG-BINDING PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomlinson, J.H. / Green, V.L. / Baker, P.J. / Williamson, M.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.9 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.8 KB | Display | ![]() |
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Full document | ![]() | 429.6 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pgaS 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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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.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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