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- PDB-6rjk: Structure of virulence factor SghA from Agrobacterium tumefaciens -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rjk | |||||||||
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Title | Structure of virulence factor SghA from Agrobacterium tumefaciens | |||||||||
![]() | Beta-glucosidase | |||||||||
![]() | HYDROLASE / Chemical signaling / Sucrose / Agrobacterium / Host-pathogen interaction / Glucosidase | |||||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ye, F.Z. / Wang, C. / Chang, C.Q. / Zhang, L.H. / Gao, Y.G. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Agrobacteria reprogram virulence gene expression by controlled release of host-conjugated signals. Authors: Wang, C. / Ye, F. / Chang, C. / Liu, X. / Wang, J. / Wang, J. / Yan, X.F. / Fu, Q. / Zhou, J. / Chen, S. / Gao, Y.G. / Zhang, L.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.6 KB | Display | ![]() |
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PDB format | ![]() | 164.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
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Full document | ![]() | 438.9 KB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rjmC ![]() 6rjoC ![]() 6rk2C ![]() 1np2S S: Starting model for refinement C: citing same article ( |
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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: Protein | Mass: 54873.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: sghA / Plasmid: pET14b-SghA / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % / Description: plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350 and 0.4 M ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Oct 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 73481 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.07 / Rrim(I) all: 0.11 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.92→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4498 / CC1/2: 0.71 / Rpim(I) all: 0.45 / Rrim(I) all: 0.66 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NP2 Resolution: 1.922→48.428 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.922→48.428 Å
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Refine LS restraints |
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LS refinement shell |
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