+Open data
-Basic information
Entry | Database: PDB / ID: 4aih | ||||||
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Title | Crystal structure of RovA from Yersinia in its free form | ||||||
Components | TRANSCRIPTIONAL REGULATOR SLYA | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / GLOBAL REGULATOR / VIRULENCE REGULATION / THERMOSENSING | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / DNA-binding transcription repressor 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: 2.4 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 | 4aih.cif.gz | 322.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aih.ent.gz | 266.7 KB | Display | PDB format |
PDBx/mmJSON format | 4aih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aih_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 4aih_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | 4aih_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 4aih_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/4aih ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4aih | HTTPS FTP |
-Related structure data
Related structure data | 4aijC 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17231.768 Da / Num. of mol.: 6 / 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: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 108 TO SER ...ENGINEERED | |
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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M MES PH 6.5, 20% PEG2000MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→90 Å / Num. obs: 36510 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DEU Resolution: 2.4→90.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.138 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 57.224 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→90.57 Å
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Refine LS restraints |
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