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Yorodumi- PDB-4ewd: Study on structure and function relationships in human Pirin with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ewd | ||||||
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Title | Study on structure and function relationships in human Pirin with Mn ion | ||||||
Components | Pirin | ||||||
Keywords | OXIDOREDUCTASE / beta sandwich / cupin / metal binding protein / transcription cofactor activity / protein binding / nucleus | ||||||
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 / Resolution: 2.15 Å | ||||||
Authors | Liu, F. / Rehmani, I. / Chen, L. / Fu, R. / Serrano, V. / Wilson, D.W. / Liu, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ewd.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ewd.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ewd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ewd_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 4ewd_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 4ewd_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4ewd_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/4ewd ftp://data.pdbj.org/pub/pdb/validation_reports/ew/4ewd | HTTPS FTP |
-Related structure data
Related structure data | 4eroC 4ewaC 4eweC 4gulC 4hltC 4ewb 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: 32159.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: human, PIR / Plasmid: PET 27A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DH5 alpha) / References: UniProt: O00625, quercetin 2,3-dioxygenase |
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#2: Chemical | ChemComp-MN / |
#3: 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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. all: 19385 / Num. obs: 17078 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.07→2.11 Å / Redundancy: 7.7 % / % possible all: 71.2 |
-Processing
Software |
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Refinement | Resolution: 2.15→26.29 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.74 / SU B: 3.478 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.049 / 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: 73 Å2 / Biso mean: 24.0741 Å2 / Biso min: 10.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→26.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
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