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Yorodumi- PDB-1irg: INTERFERON REGULATORY FACTOR-2 DNA BINDING DOMAIN, NMR, 20 STRUCTURES -
+Open data
-Basic information
Entry | Database: PDB / ID: 1irg | ||||||
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Title | INTERFERON REGULATORY FACTOR-2 DNA BINDING DOMAIN, NMR, 20 STRUCTURES | ||||||
Components | INTERFERON REGULATORY FACTOR-2 | ||||||
Keywords | TRANSCRIPTION REGULATION / WINGED HELIX-TURN-HELIX | ||||||
Function / homology | Function and homology information toll-like receptor 3 signaling pathway / immune system process / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / focal adhesion / regulation of transcription by RNA polymerase II / nucleoplasm ...toll-like receptor 3 signaling pathway / immune system process / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / focal adhesion / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Furui, J. / Uegaki, K. / Yamazaki, T. / Shirakawa, M. / Swindells, M.B. / Harada, H. / Taniguchi, T. / Kyogoku, Y. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family. Authors: Furui, J. / Uegaki, K. / Yamazaki, T. / Shirakawa, M. / Swindells, M.B. / Harada, H. / Taniguchi, T. / Kyogoku, Y. #1: Journal: FEBS Lett. / Year: 1995 Title: Secondary Structure and Folding Topology of the DNA Binding Domain of Interferon Regulatory Factor 2, as Revealed by NMR Spectroscopy Authors: Uegaki, K. / Shirakawa, M. / Harada, H. / Taniguchi, T. / Kyogoku, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1irg.cif.gz | 734.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1irg.ent.gz | 614.8 KB | Display | PDB format |
PDBx/mmJSON format | 1irg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1irg_validation.pdf.gz | 346 KB | Display | wwPDB validaton report |
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Full document | 1irg_full_validation.pdf.gz | 554.5 KB | Display | |
Data in XML | 1irg_validation.xml.gz | 82.3 KB | Display | |
Data in CIF | 1irg_validation.cif.gz | 107.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/1irg ftp://data.pdbj.org/pub/pdb/validation_reports/ir/1irg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13354.515 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 - 113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Cellular location: NUCLEUS / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (LAMBDA DE3) / References: UniProt: P23906 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 5.70 / Temperature: 298.00 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: STRUCTURAL STATISTICS: AVERAGE SD RMSD FROM EXPERIMENTAL DISTANCE RESTRAINTS ALL (1453) 0.025 A 0.001 A INTRARESIDUE NOE (415) 0.022 A 0.001 A SEQUENTIAL NOE (|I-J|=1) (381) 0.025 A 0.003 A MEDIUM RANGE NOE (1<|I-J|<5) (242) 0.026 A 0.004 A LONG RANGE NOE (|I-J|>=5) (363) 0.022 A 0.003 A HYDROGEN BOND (52)* 0.051 A 0.002 A | ||||||||||||
NMR ensemble | Conformer selection criteria: THE LOWEST TARGET FUNCTIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20 |