+Open data
-Basic information
Entry | Database: PDB / ID: 7fby | ||||||
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Title | Crystal Structure of PH0140 from Pyrococcus horikosii OT3 | ||||||
Components | Transcriptional regulatory protein | ||||||
Keywords | TRANSCRIPTION / transcriptional regulator | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Richard, M. / Ahmad, M. / Pal, R.K. / Biswal, B.K. / Jeyakanthan, J. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of PH0140 from Pyrococcus horikosii OT3 Authors: Richard, M. / Ahmad, M. / Pal, R.K. / Biswal, B.K. / Jeyakanthan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fby.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fby.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 7fby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fby_validation.pdf.gz | 739.3 KB | Display | wwPDB validaton report |
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Full document | 7fby_full_validation.pdf.gz | 741.1 KB | Display | |
Data in XML | 7fby_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7fby_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/7fby ftp://data.pdbj.org/pub/pdb/validation_reports/fb/7fby | HTTPS FTP |
-Related structure data
Related structure data | 2cyyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 18783.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT-3 / Gene: PH0140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O57880 | ||||
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#2: Chemical | ChemComp-ILE / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1 M HEPES (PH 7.5), 4.3 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 12806 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.54 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 1258 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CYY Resolution: 2.001→25.711 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.096 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.144 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.418 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→25.711 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 31.6751 Å / Origin y: 30.4912 Å / Origin z: 73.033 Å
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Refinement TLS group | Selection: ALL |