+Open data
-Basic information
Entry | Database: PDB / ID: 4qqi | ||||||
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Title | Crystal structure of ANKRA2-RFX7 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / RNA polymerase II core promoter sequence-specific DNA binding / histone deacetylase binding / sequence-specific double-stranded DNA binding / regulation of gene expression / cytoskeleton / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ubiquitin protein ligase binding ...low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / RNA polymerase II core promoter sequence-specific DNA binding / histone deacetylase binding / sequence-specific double-stranded DNA binding / regulation of gene expression / cytoskeleton / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å | ||||||
Authors | Xu, C. / Tempel, W. / Dong, A. / Mackenzie, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of ANKRA2-RFX7 complex Authors: Xu, C. / Tempel, W. / Mackenzie, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qqi.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qqi.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 4qqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/4qqi ftp://data.pdbj.org/pub/pdb/validation_reports/qq/4qqi | HTTPS FTP |
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-Related structure data
Related structure data | 3so8S 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
-Protein / Protein/peptide , 2 types, 2 molecules AX
#1: Protein | Mass: 20927.602 Da / Num. of mol.: 1 / Fragment: UNP residues 142-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA2, ANKRA / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9H9E1 |
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#2: Protein/peptide | Mass: 2000.364 Da / Num. of mol.: 1 / Fragment: UNP residues 85-101 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q2KHR2 |
-Non-polymers , 4 types, 95 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #6: Water | ChemComp-HOH / | |
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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: 3 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M sodium hepes, 2.0 M ammonium sulfate, 2% PEG 400, pH 7.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||
Detector | Type: R-Axis / Detector: IMAGE PLATE / Date: May 14, 2013 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.02→37.73 Å / Num. obs: 17145 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 10.5 | ||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.01 / Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3so8 Resolution: 2.03→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2258 / WRfactor Rwork: 0.1818 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7444 / SU B: 6.041 / SU ML: 0.152 / SU R Cruickshank DPI: 0.1858 / SU Rfree: 0.1765 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ARP/WARP was used for phase improvement and automated model building. COOT and MOLPROBITY were also used during refinement.
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.46 Å2 / Biso mean: 24.7826 Å2 / Biso min: 5.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.082 Å / Total num. of bins used: 20
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