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- PDB-4aik: Crystal structure of RovA from Yersinia in complex with an invasi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aik | ||||||
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Title | Crystal structure of RovA from Yersinia in complex with an invasin promoter fragment | ||||||
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![]() | TRANSCRIPTION / TRANSCRIPTION FACTOR / GLOBAL REGULATOR / VIRULENCE REGULATION / THERMOSENSING | ||||||
Function / homology | ![]() response to stress / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Quade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Heinz, D.W. / Dersch, P. | ||||||
![]() | ![]() Title: Structural Basis for Intrinsic Thermosensing by the Master Virulence Regulator Rova of Yersinia. Authors: Quade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Ritter, C. / Heinz, D.W. / Dersch, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.9 KB | Display | ![]() |
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PDB format | ![]() | 140.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.8 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aihC ![]() 4aijC ![]() 3deuS C: citing same article ( 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.49888, -0.86666, -0.00313), Vector: |
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Components
#1: Protein | Mass: 17231.768 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 6474.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | | Mass: 6403.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 108 TO SER ...ENGINEERED | Sequence details | GB AAK01704.1 PROTEIN, GB NC_010465.1 DNA | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 10 MM MGCL2, 50 MM MES PH 5.6, 2.3 M LISO4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 28, 2010 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.85→76 Å / Num. obs: 49796 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 13.9 | |||||||||||||||
Reflection shell | Resolution: 1.85→2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7414 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DEU Resolution: 1.85→76.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.557 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.024 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.527 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→76.81 Å
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Refine LS restraints |
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