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Yorodumi- PDB-3acl: Crystal Structure of Human Pirin in complex with Triphenyl Compound -
+Open data
-Basic information
Entry | Database: PDB / ID: 3acl | ||||||
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Title | Crystal Structure of Human Pirin in complex with Triphenyl Compound | ||||||
Components | Pirin | ||||||
Keywords | METAL BINDING PROTEIN / cupin / inhibitor / complex / Iron | ||||||
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 / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Okumura, H. / Miyazaki, I. / Simizu, S. / Osada, H. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2010 Title: A small-molecule inhibitor shows that pirin regulates migration of melanoma cells Authors: Miyazaki, I. / Simizu, S. / Okumura, H. / Takagi, S. / Osada, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3acl.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3acl.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 3acl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3acl_validation.pdf.gz | 691.5 KB | Display | wwPDB validaton report |
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Full document | 3acl_full_validation.pdf.gz | 696.9 KB | Display | |
Data in XML | 3acl_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 3acl_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/3acl ftp://data.pdbj.org/pub/pdb/validation_reports/ac/3acl | HTTPS FTP |
-Related structure data
Related structure data | 1j1lS 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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Unit cell |
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-Components
#1: Protein | Mass: 32988.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIR / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O00625 |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-3F1 / |
#4: 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: 2.33 Å3/Da / Density % sol: 47.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 34% PEG 3350, 0.1M PIPES, 0.1M MGCL2, 1.4mM INHIBITOR, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 19, 2009 |
Diffraction measurement | Details: 1.00 degrees, 31.2 sec, detector distance 200.00mm |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.127 / Number: 13541 |
Reflection | Resolution: 2.35→50 Å / Num. all: 13554 / Num. obs: 13541 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.803 / Rsym value: 0.34 / % possible all: 100 |
Cell measurement | Reflection used: 13541 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J1L Resolution: 2.35→35.86 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1297395 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.223 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.33 Å2 / Biso mean: 19.79 Å2 / Biso min: 1.01 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→35.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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