+Open data
-Basic information
Entry | Database: PDB / ID: 3t22 | ||||||
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Title | Crystal structure of OxyR mutant from Porphyromonas gingivalis | ||||||
Components | Redox-sensitive transcriptional activator OxyR | ||||||
Keywords | TRANSCRIPTION REGULATOR / beta-alpha-barrels / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Svintradze, D.V. / Wright, H.T. / Lewis, J.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis. Authors: Svintradze, D.V. / Peterson, D.L. / Collazo-Santiago, E.A. / Lewis, J.P. / Wright, H.T. #1: Journal: To be Published Title: The iron-oxygen molecular switch in the anaerobic bacterium Porphyromonas gingivalis Authors: Lewis, J.P. / Yanamandra, S. / Ghosh, A.K. / Svintradze, D.V. / Sengupta, D. / Jones, K. / Iyer, D. / Peterson, D. / Wright, H.T. / Anaya-Bergman, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t22.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t22.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 3t22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/3t22 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/3t22 | HTTPS FTP |
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-Related structure data
Related structure data | 3ho7SC 3ukiC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25605.510 Da / Num. of mol.: 4 / Fragment: Regulatory domain (UNP residues 90-308) / Mutation: C199S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: oxyR / Production host: Escherichia coli (E. coli) / References: UniProt: Q20K61 #2: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 30% PEG 3000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2011 |
Radiation | Monochromator: MSC Varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→23.24 Å / Num. obs: 69702 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.53 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 0.9 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HO7 Resolution: 2.2→18.358 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 31.7 / Stereochemistry target values: ML Details: The structure factor file contains 69444 reflections with the resolution range of 1.90-23.24 A. However the resolution of 2.2-18.358 A with 44680 reflections was used for the refinement. The ...Details: The structure factor file contains 69444 reflections with the resolution range of 1.90-23.24 A. However the resolution of 2.2-18.358 A with 44680 reflections was used for the refinement. The decision of cutting the high resolution reflections was based on the low intensity signals for 1.90 A resolution which were keeping R factor high during the refinement.
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.001 Å2 / ksol: 0.344 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→18.358 Å
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Refine LS restraints |
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LS refinement shell |
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