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Yorodumi- PDB-2ovg: Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ovg | ||||||
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Title | Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221 | ||||||
Components | Phage lambda Cro | ||||||
Keywords | TRANSCRIPTION / Transcription factor / helix-turn-helix / bacteriophage / flexibility | ||||||
Function / homology | Function and homology information latency-replication decision / release from viral latency / negative regulation of transcription by competitive promoter binding / negative regulation of viral transcription / core promoter sequence-specific DNA binding / response to UV / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Hall, B.M. / Heroux, A. / Roberts, S.A. / Cordes, M.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA. Authors: Hall, B.M. / Roberts, S.A. / Heroux, A. / Cordes, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ovg.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ovg.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ovg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/2ovg ftp://data.pdbj.org/pub/pdb/validation_reports/ov/2ovg | HTTPS FTP |
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-Related structure data
Related structure data | 2ecsC 6croS 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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2 |
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3 |
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Unit cell |
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Details | The asymmetric unit contains a monomer which is half of the biological assembly. The second part of the biological assembly is generated by the two fold axis: -x, y-x, 2/3-z |
-Components
#1: Protein | Mass: 7359.418 Da / Num. of mol.: 1 / Mutation: Q27P, A29S, K32Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: cro / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03040 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-EPE / |
#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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M lithium sulfate, 0.1 M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2005 / Details: mirrors |
Radiation | Monochromator: Si (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 15657 / Num. obs: 15657 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.941 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.96 / Num. unique all: 1513 / Χ2: 1.719 / % possible all: 96.5 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6CRO protein portion Resolution: 1.35→43.77 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.494 / SU ML: 0.028 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.048 / 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: 9.781 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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