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Yorodumi- PDB-3v30: Crystal Structure of the Peptide Bound Complex of the Ankyrin Rep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v30 | ||||||
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Title | Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human RFXANK | ||||||
Components |
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Keywords | PROTEIN BINDING / Structural Genomics Consortium / SGC / RFXANK / ANK repeat / RFX5 | ||||||
Function / homology | Function and homology information positive regulation of MHC class II biosynthetic process / intercellular bridge / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / histone deacetylase binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Ras protein signal transduction / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...positive regulation of MHC class II biosynthetic process / intercellular bridge / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / histone deacetylase binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Ras protein signal transduction / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å | ||||||
Authors | Lam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci.Signal. / Year: 2012 Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock. Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v30.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v30.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3v30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/3v30 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v30 | HTTPS FTP |
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-Related structure data
Related structure data | 3so8SC 3uxgC 3uzdC 3v2oC 3v2xC 3v31C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18926.301 Da / Num. of mol.: 1 / Fragment: UNP residues 90-260 (ANK repeats) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA1, RFXANK, RFXB / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: O14593 |
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#2: Protein/peptide | Mass: 1755.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in human RFX5. / Source: (synth.) Homo sapiens (human) / References: UniProt: P48382 |
#3: 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: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010 Details: Rosenbaum-Rock high-resolution double-crystal monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→50 Å / Num. obs: 28759 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.039 / Χ2: 0.997 / Net I/σ(I): 27.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SO8 Resolution: 1.57→46.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.339 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.96 Å2 / Biso mean: 15.4991 Å2 / Biso min: 6.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→46.88 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: 20
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