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Yorodumi- PDB-4aij: Crystal structure of RovA from Yersinia in complex with a rovA pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aij | ||||||
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Title | Crystal structure of RovA from Yersinia in complex with a rovA promoter fragment | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / GLOBAL REGULATOR / VIRULENCE REGULATION / THERMOSENSING | ||||||
Function / homology | Function and homology information 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 | YERSINIA PSEUDOTUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Quade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Heinz, D.W. / Dersch, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aij.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aij.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 4aij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/4aij ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4aij | HTTPS FTP |
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-Related structure data
Related structure data | 4aihC 4aikC 3deuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99997, -0.00456, -0.00695), Vector: |
-Components
#1: Protein | Mass: 17231.768 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B1JJ73 #2: DNA chain | | Mass: 6449.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) #3: DNA chain | | Mass: 6427.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) #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 | CROSS-REFERENCE FOR DNA SEQUENCE IS NC_010465.1 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95 | |||||||||||||||
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: 2.1→37 Å / Num. obs: 39678 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 15.3 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DEU Resolution: 2.05→76.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.561 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / 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: 65.609 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→76.9 Å
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Refine LS restraints |
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