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- PDB-7cdx: Complex STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cdx | |||||||||
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Title | Complex STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR with its effector sucrose | |||||||||
![]() | LacI-type transcription factor | |||||||||
![]() | TRANSCRIPTION / AGROBACTERIUM INFECTION / PLANT-MICROBE INTERACTION / LACI REP SUCROSE | |||||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ye, F.Z. / Wang, C. / Yan, X.F. / Zhang, L.H. / Gao, Y.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of a novel repressor, SghR, controllingAgrobacteriuminfection by cross-talking to plants. Authors: Ye, F. / Wang, C. / Fu, Q. / Yan, X.F. / Bharath, S.R. / Casanas, A. / Wang, M. / Song, H. / Zhang, L.H. / Gao, Y.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.7 KB | Display | ![]() |
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PDB format | ![]() | 95.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cdvSC ![]() 7ce1C 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: 40776.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: sghR Production host: ![]() ![]() References: UniProt: A0A2I4PGE9 #2: Polysaccharide | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.61 Å3/Da / Density % sol: 23.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05M HEPES-Na pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9985 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 58464 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rpim(I) all: 0.09 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.1→2.23 Å / Num. unique obs: 31106 / Rsym value: 0.41 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CDV Resolution: 2.103→42.832 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 34.92 / 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: 64.24 Å2 / Biso mean: 21.18 Å2 / Biso min: 3.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.103→42.832 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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