+Open data
-Basic information
Entry | Database: PDB / ID: 6n0k | ||||||
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Title | The complex of CCG-257081 bound to pirin | ||||||
Components | Pirin | ||||||
Keywords | OXIDOREDUCTASE / beta barrel / iron-binding / co-transcription factor | ||||||
Function / homology | Function and homology information Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / nucleus ...Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Lisabeth, E.M. / Jin, X. / Neubig, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Pharmacol Transl Sci / Year: 2019 Title: Identification of Pirin as a Molecular Target of the CCG-1423/CCG-203971 Series of Antifibrotic and Antimetastatic Compounds Authors: Lisabeth, E.M. / Kahl, D. / Gopallawa, I. / Haynes, S.E. / Misek, S.A. / Campbell, P.L. / Dexheimer, T.S. / Khanna, D. / Fox, D.A. / Jin, X. / Martin, B.R. / Larsen, S.D. / Neubig, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n0k.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n0k.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 6n0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/6n0k ftp://data.pdbj.org/pub/pdb/validation_reports/n0/6n0k | HTTPS FTP |
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-Related structure data
Related structure data | 6n0jC 5jctS 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: 33433.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIR / Production host: Escherichia coli (E. coli) / References: UniProt: O00625, quercetin 2,3-dioxygenase | ||
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#2: Chemical | ChemComp-FE / | ||
#3: Chemical | ChemComp-K8M / ( | ||
#4: Chemical | ChemComp-EDO / #5: 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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M Hepes pH 7.5, 8% Ethylene Glycol, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→35.75 Å / Num. obs: 53779 / % possible obs: 99.57 % / Redundancy: 6.2 % / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2 / Num. unique obs: 5202 / Rpim(I) all: 0.229 / Rrim(I) all: 0.548 / % possible all: 97.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5jct Resolution: 1.46→35.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→35.75 Å
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Refine LS restraints |
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LS refinement shell |
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