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- PDB-3geu: Crystal Structure of IcaR from Staphylococcus aureus, a member of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3geu | ||||||
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Title | Crystal Structure of IcaR from Staphylococcus aureus, a member of the tetracycline repressor protein family | ||||||
![]() | Intercellular adhesion protein R | ||||||
![]() | CELL ADHESION / TetR family / intercellular adhesion regulator / IDP00851 / DNA-binding / Repressor / Transcription / Transcription regulation / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Anderson, S.M. / Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Papazisi, L. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Crystal Structure of IcaR from Staphylococcus aureus, a member of the tetracycline repressor protein family Authors: Anderson, S.M. / Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Papazisi, L. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.5 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.8 KB | Display | ![]() |
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Full document | ![]() | 484.3 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22517.777 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: PEG3350 20%, 0.2M NH4 Formate, pH 7, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 67790 / Num. obs: 67319 / % possible obs: 99.3 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.4 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6284 / % possible all: 93.7 |
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Processing
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Refinement | Resolution: 1.9→40.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.632 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.145 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 231.67 Å2 / Biso mean: 35.916 Å2 / Biso min: 8.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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