+Open data
-Basic information
Entry | Database: PDB / ID: 6p0q | ||||||
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Title | Crystal Structure of Ubiquitin-like Domain of Human WDR12 | ||||||
Components | Ribosome biogenesis protein WDR12 | ||||||
Keywords | RNA BINDING PROTEIN / Ubiquitin-like Domain / WDR12 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Notch signaling pathway / ribosomal large subunit biogenesis / regulation of cell cycle / nucleolus / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å | ||||||
Authors | Halabelian, L. / Dong, A. / Zeng, H. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal Structure of Ubiquitin-like Domain of Human WDR12 Authors: Halabelian, L. / Dong, A. / Zeng, H. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p0q.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p0q.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 6p0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/6p0q ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p0q | HTTPS FTP |
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-Related structure data
Related structure data | 5dtcS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11115.585 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR12 / Plasmid: pNIC-CTHO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9GZL7 #2: Chemical | ChemComp-EDO / #3: 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: 2.25 Å3/Da / Density % sol: 45.32 % / Mosaicity: 0.724 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.5M NH4SO4, 0.1M NaOAc pH4.6 |
-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: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 4, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→50 Å / Num. obs: 20767 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Χ2: 1.31 / Net I/σ(I): 10.7 / Num. measured all: 117773 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 5DTC Resolution: 1.72→23.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.234 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.119 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.77 Å2 / Biso mean: 14.779 Å2 / Biso min: 5.38 Å2
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Refinement step | Cycle: final / Resolution: 1.72→23.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.721→1.766 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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