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- PDB-4gul: Study on structure and function relationships in human ferric Pirin -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gul | ||||||
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Title | Study on structure and function relationships in human ferric Pirin | ||||||
![]() | Pirin | ||||||
![]() | SIGNALING PROTEIN / beta sandwich / cupin / iron / metal binding protein / transcription cofactor activity / protein binding | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, F. / Rehmani, I. / Fu, R. / Esaka, S. / Chen, L. / Serrano, V. / Liu, A. | ||||||
![]() | ![]() Title: Pirin is an iron-dependent redox regulator of NF-kappa B. Authors: Liu, F. / Rehmani, I. / Esaki, S. / Fu, R. / Chen, L. / de Serrano, V. / Liu, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.5 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 431.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4eroC ![]() 4ewaC ![]() 4ewdC ![]() 4eweC ![]() 4hltC ![]() 1j1lS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31971.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 20000, 0.1 MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→21.88 Å / Num. all: 27328 / Num. obs: 25931 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 32.93 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible all: 67.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J1L Resolution: 1.8→21.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.073 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.23 Å2 / Biso mean: 21.715 Å2 / Biso min: 8.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→21.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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