+Open data
-Basic information
Entry | Database: PDB / ID: 3k79 | ||||||
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Title | C38A, C52V Cysteine-Free Variant of Rop (Rom) | ||||||
Components | Regulatory protein rop | ||||||
Keywords | TRANSCRIPTION / hairpin / four-helix bundle / cysteine-free / Plasmid / Transcription regulation | ||||||
Function / homology | Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å | ||||||
Authors | Hari, S.B. / Magliery, T.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Cysteine-free Rop: a four-helix bundle core mutant has wild-type stability and structure but dramatically different unfolding kinetics. Authors: Hari, S.B. / Byeon, C. / Lavinder, J.J. / Magliery, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k79.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k79.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 3k79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k79_validation.pdf.gz | 407.2 KB | Display | wwPDB validaton report |
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Full document | 3k79_full_validation.pdf.gz | 407.2 KB | Display | |
Data in XML | 3k79_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 3k79_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/3k79 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/3k79 | HTTPS FTP |
-Related structure data
Related structure data | 1ropS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7126.818 Da / Num. of mol.: 1 / Mutation: C38A, C52V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pMR101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03051 |
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#2: 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: 1.96 Å3/Da / Density % sol: 37.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 25-30% methanol, 100 mM MES, 300 mM NaCl, 10% glycerol, pH 5.7-5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 5.7-5.9 |
-Data collection
Diffraction | Mean temperature: 113 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 7, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→29.63 Å / Num. obs: 2675 / % possible obs: 66.1 % / Redundancy: 7.26 % / Rmerge(I) obs: 0.032 / Χ2: 0.97 / Net I/σ(I): 47.4 / Scaling rejects: 147 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 39.53 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ROP Resolution: 1.96→29.63 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.768 / SU ML: 0.31 / σ(F): 2.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.655 Å2 / ksol: 0.459 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.5 Å2 / Biso mean: 26.236 Å2 / Biso min: 11.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→29.63 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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