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- PDB-4at8: Crystal structure of the NF90-NF45 dimerisation domain complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4at8 | ||||||
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Title | Crystal structure of the NF90-NF45 dimerisation domain complex with ATP | ||||||
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![]() | TRANSCRIPTION / DRPB76 / NFAR / ILF3 / ILF2 / TEMPLATE-FREE NUCLEOTIDYLTRANSFERASE FOLD | ||||||
Function / homology | ![]() Regulation of CDH11 gene transcription / PKR-mediated signaling / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / precatalytic spliceosome / Neutrophil degranulation / catalytic step 2 spliceosome / double-stranded RNA binding / virus receptor activity / defense response to virus ...Regulation of CDH11 gene transcription / PKR-mediated signaling / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / precatalytic spliceosome / Neutrophil degranulation / catalytic step 2 spliceosome / double-stranded RNA binding / virus receptor activity / defense response to virus / single-stranded RNA binding / negative regulation of translation / ribonucleoprotein complex / protein phosphorylation / negative regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wolkowicz, U.M. / Cook, A.G. | ||||||
![]() | ![]() Title: NF45 Dimerizes with NF90, Zfr and Spnr Via a Conserved Domain that Has a Nucleotidyltransferase Fold. Authors: Wolkowicz, U.M. / Cook, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.5 KB | Display | ![]() |
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PDB format | ![]() | 202.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.8 KB | Display | |
Data in CIF | ![]() | 61.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4at7SC ![]() 4at9C ![]() 4atbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.59248, 0.00139, 0.80558), Vector: |
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Components
#1: Protein | Mass: 40359.840 Da / Num. of mol.: 2 / Fragment: DZF DOMAIN, RESIDUES 29-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 42526.727 Da / Num. of mol.: 2 / Fragment: DZF DOMAIN, RESIDUES 1-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | Sequence details | TWO RESIDUES ADDED AT N-TERMINUS OF CHAIN A DERIVED FROM PRESCISSION CLEAVAGE SITE. TWO RESIDUES AT ...TWO RESIDUES ADDED AT N-TERMINUS OF CHAIN A DERIVED FROM PRESCISSIO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 12-14 % PEG3350, 200 MM MGCL2, 100 MM MES PH 6.5, 5 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2011 / Details: TOROIDAL MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→66 Å / Num. obs: 50589 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 34.19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.69→2.84 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AT7 Resolution: 2.692→57.844 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 26.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.221 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.692→57.844 Å
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Refine LS restraints |
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LS refinement shell |
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