+Open data
-Basic information
Entry | Database: PDB / ID: 3gn5 | ||||||
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Title | Structure of the E. coli protein MqsA (YgiT/b3021) | ||||||
Components | (HTH-type transcriptional regulator MQSA (YGIT/b3021)) x 2 | ||||||
Keywords | DNA BINDING PROTEIN / Zn-binding protein / HTH-XRE DNA binding motif / DNA-binding / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information toxin-antitoxin complex / single-species biofilm formation / sequence-specific DNA binding / regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Brown, B.L. / Arruda, J.M. / Peti, W. / Page, R. | ||||||
Citation | Journal: Plos Pathog. / Year: 2009 Title: Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties. Authors: Brown, B.L. / Grigoriu, S. / Kim, Y. / Arruda, J.M. / Davenport, A. / Wood, T.K. / Peti, W. / Page, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gn5.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gn5.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gn5_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 3gn5_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 3gn5_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 3gn5_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gn5 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gn5 | HTTPS FTP |
-Related structure data
Related structure data | 3fmySC 3ga8SC 3hi2C 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: 14923.341 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: Escherichia coli str. K12 / Gene: b3021, JW2989, ygiT / Plasmid: RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 RIL / References: UniProt: Q46864 | ||||
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#2: Protein | Mass: 14937.368 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: Escherichia coli str. K12 / Gene: ygiT, b3021, JW2989 / Plasmid: RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 RIL / References: UniProt: Q46864 | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.33 Å3/Da / Density % sol: 47.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis-Tris, 0.2M magnesium chloride hexahydrate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2009 / Details: toroidal focusing mirror |
Radiation | Monochromator: Si (111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 15447 / Num. obs: 15349 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.074 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.85 / Num. unique all: 759 / Rsym value: 0.271 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 3GA8 and 3FMY Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.417 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.248 / ESU R Free: 0.199 / 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 mean: 21.319 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.202 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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