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Yorodumi- PDB-4fc8: Crystal structure of transcription regulator protein Rtr1 from Kl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fc8 | ||||||
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Title | Crystal structure of transcription regulator protein Rtr1 from Kluyveromyces lactis | ||||||
Components | transcription protein Rtr1 | ||||||
Keywords | TRANSCRIPTION / zinc finger | ||||||
Function / homology | Function and homology information RNA polymerase II CTD heptapeptide repeat phosphatase activity / RNA polymerase core enzyme binding / myosin phosphatase activity / protein-serine/threonine phosphatase / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Xiang, K. / Tong, L. | ||||||
Citation | Journal: Nat Commun / Year: 2012 Title: The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity. Authors: Xiang, K. / Manley, J.L. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fc8.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fc8.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 4fc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fc8 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fc8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Two molecules in one asymmetric unit |
-Components
#1: Protein | Mass: 25780.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0F12672g, KLLA0_F12672g / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q6CK86 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THE FOLLOWING: THE FULL-LENGTH PROTEIN WAS DEGRADED DURING CRYSTALLIZATION, CONFIRMED ...AUTHORS STATE THE FOLLOWING: THE FULL-LENGTH PROTEIN WAS DEGRADED DURING CRYSTALLIZ | |
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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: 1.84 Å3/Da / Density % sol: 33.24 % |
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Crystal grow | Temperature: 293 K / pH: 9.5 Details: 0.1M CHES pH 9.5 20% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.2833, 1.2836, 1.2652 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2011 | ||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 24945 / % possible obs: 99.1 % / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.041 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.292 / 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: 57.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.63 Å / Total num. of bins used: 10
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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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