+Open data
-Basic information
Entry | Database: PDB / ID: 7da8 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of a GB1:T2Q/D46K mutant | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | PROTEIN BINDING / GB1 / T2Q mutant / D46K mutant / X-ray crystal structure / PLANT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. group G (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
Citation | Journal: To Be Published Title: X-ray structure of a GB1:T2Q/D46K mutant Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7da8.cif.gz | 23.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7da8.ent.gz | 13 KB | Display | PDB format |
PDBx/mmJSON format | 7da8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7da8_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7da8_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 7da8_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 7da8_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7da8 ftp://data.pdbj.org/pub/pdb/validation_reports/da/7da8 | HTTPS FTP |
-Related structure data
Related structure data | 1pgbS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 26.03 % |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54187 Å | ||||||||||||||||||||||||||||||
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
|
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||
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
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.406→30.81 Å / Rfactor Rfree error: 0
|