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Open data
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Basic information
Entry | Database: PDB / ID: 7da8 | ||||||
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Title | X-ray structure of a GB1:T2Q/D46K mutant | ||||||
![]() | Immunoglobulin G-binding protein G | ||||||
![]() | PROTEIN BINDING / GB1 / T2Q mutant / D46K mutant / X-ray crystal structure / PLANT PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
![]() | ![]() Title: X-ray structure of a GB1:T2Q/D46K mutant Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.3 KB | Display | ![]() |
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PDB format | ![]() | 13 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pgbS 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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Unit cell |
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Components
#1: Antibody | Mass: 7071.782 Da / Num. of mol.: 1 / Mutation: T303Q, D347K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 26.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MES monohydrate pH 6.5 (buffer system 1), 40% v/v PEG 500* MME, 20 % w/v PEG 20000 (Precipitant mix1) (Morpheus Screen ID 25). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 6, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→30.82 Å / Num. obs: 2003 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.093 / Rrim(I) all: 0.233 / Net I/σ(I): 5.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1pgb Resolution: 2.4→30.819 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.17 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 76.7 Å2 / Biso mean: 33.7382 Å2 / Biso min: 12.19 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→30.819 Å
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LS refinement shell | Resolution: 2.406→30.81 Å / Rfactor Rfree error: 0
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