+Open data
-Basic information
Entry | Database: PDB / ID: 1gv2 | ||||||
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Title | CRYSTAL STRUCTURE OF C-MYB R2R3 | ||||||
Components | MYB PROTO-ONCOGENE PROTEIN | ||||||
Keywords | TRANSCRIPTION / MYB / C-MYB / DNA BINDING / ION BINDING | ||||||
Function / homology | Function and homology information positive regulation of testosterone secretion / myeloid cell development / positive regulation of hepatic stellate cell proliferation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / embryonic digestive tract development / stem cell division / myeloid cell differentiation / cellular response to interleukin-6 / WD40-repeat domain binding ...positive regulation of testosterone secretion / myeloid cell development / positive regulation of hepatic stellate cell proliferation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / embryonic digestive tract development / stem cell division / myeloid cell differentiation / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / positive regulation of collagen biosynthetic process / positive regulation of glial cell proliferation / spleen development / B cell differentiation / thymus development / cellular response to leukemia inhibitory factor / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / calcium ion transport / positive regulation of neuron apoptotic process / mitotic cell cycle / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus Musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Tahirov, T.H. / Ogata, K. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of C-Myb DNA-Binding Domain: Specific Na+ Binding and Correlation with NMR Structure Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sasaki, M. / Sarai, A. / Adachi, S. / Park, S.Y. / Kamiya, N. / Ogata, K. #1: Journal: Cell (Cambridge,Mass.) / Year: 2002 Title: Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter Authors: Tahirov, T.H. / Sato, K. / Ichikawa-Iwata, E. / Sasaki, M. / Inoue-Bungo, T. / Shiina, M. / Kimura, K. / Takata, S. / Fujikawa, A. / Morii, H. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gv2.cif.gz | 37 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gv2.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gv2_validation.pdf.gz | 402.4 KB | Display | wwPDB validaton report |
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Full document | 1gv2_full_validation.pdf.gz | 403 KB | Display | |
Data in XML | 1gv2_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1gv2_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gv2 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gv2 | HTTPS FTP |
-Related structure data
Related structure data | 1guuC 1gv5C 1gvdC 1mbgS 1mbjS C: citing same article (ref.) 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: 12674.693 Da / Num. of mol.: 1 / Fragment: R2R3, RESIDUES 89-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus Musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06876 | ||
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#2: Chemical | #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: 1.9 Å3/Da / Density % sol: 35.4 % |
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Crystal grow | pH: 6.8 Details: 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED ...Details: 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO SODIUM CITRATE TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 29, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 11033 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.244 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.601 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.904 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1MBG AND 1MBJ Resolution: 1.68→44.12 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 87837.03 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1365 Å2 / ksol: 0.357663 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.68→44.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.79 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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