+Open data
-Basic information
Entry | Database: PDB / ID: 4af5 | ||||||
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Title | Structure of the C. glutamicum AcnR Crystal Form I | ||||||
Components | HTH-TYPE TRANSCRIPTIONAL REPRESSOR ACNR COMPND 2 | ||||||
Keywords | TRANSCRIPTION / ACONITASE / TETR REPRESSOR | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | CORYNEBACTERIUM GLUTAMICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Garcia-Nafria, J. / Baumgart, M. / Turkenburg, J.P. / Wilkinson, A.J. / Bott, M. / Wilson, K.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal and Solution Studies Reveal that the Transcriptional Regulator Acnr of Corynebacterium Glutamicum is Regulated by Citrate:Mg2+ Binding to a Non-Canonical Pocket. Authors: Garcia-Nafria, J. / Baumgart, M. / Turkenburg, J.P. / Wilkinson, A.J. / Bott, M. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: The Corynebacterium Glutamicum Aconitase Repressor: Scratching Around for Crystals. Authors: Garcia-Nafria, J. / Baumgart, M. / Bott, M. / Wilkinson, A.J. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4af5.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4af5.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 4af5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/4af5 ftp://data.pdbj.org/pub/pdb/validation_reports/af/4af5 | HTTPS FTP |
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-Related structure data
Related structure data | 4ac6SC 4aciC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 21412.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NQ97 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 42.9 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 1 M AMMONIUM PHOSPHATE; 100 MM SODIUM CITRATE PH 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.31 Å / Num. obs: 15067 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AC6 Resolution: 1.9→73.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.081 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 24.792 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→73.2 Å
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Refine LS restraints |
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