+Open data
-Basic information
Entry | Database: PDB / ID: 1gvd | ||||||
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Title | CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT | ||||||
Components | MYB PROTO-ONCOGENE PROTEIN | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / MYB / C-MYB / DNA BINDING / ION BINDING / PROTO-ONCOGENE / NUCLEAR PROTEIN | ||||||
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 / negative regulation of hematopoietic progenitor cell differentiation / positive regulation of transforming growth factor beta production / embryonic digestive tract development / stem cell division / myeloid cell differentiation / cellular response to interleukin-6 ...positive regulation of testosterone secretion / myeloid cell development / positive regulation of hepatic stellate cell proliferation / positive regulation of hepatic stellate cell activation / negative regulation of hematopoietic progenitor cell differentiation / positive regulation of transforming growth factor beta production / embryonic digestive tract development / stem cell division / myeloid cell differentiation / cellular response to interleukin-6 / T-helper 2 cell differentiation / WD40-repeat domain binding / homeostasis of number of cells / positive regulation of collagen biosynthetic process / negative regulation of megakaryocyte differentiation / positive regulation of glial cell proliferation / spleen development / cellular response to leukemia inhibitory factor / erythrocyte differentiation / B cell differentiation / thymus development / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / positive regulation of neuron apoptotic process / calcium ion transport / 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 / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / 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 / MOLECULAR REPLACEMENT / Resolution: 1.45 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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-Ray Analysis of Wild Type and V103L Mutant Myb R2 DNA-Binding Domain Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sarai, A. / Ogata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gvd.cif.gz | 25.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gvd.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvd ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvd | HTTPS FTP |
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-Related structure data
Related structure data | 1guuC 1gv2C 1gv5SC 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: 6316.437 Da / Num. of mol.: 1 / Fragment: R2, RESIDUES 90-141 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P06876 | ||||
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#2: Chemical | ChemComp-NH4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 297 K / pH: 6.8 Details: 3.15 M AMMONIUM SULFATE IN 0.05 M MES BUFFER AT PH 6.8, PROTEIN CONCENTRATION 10 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MAC SCIENCE M06XHF22 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jul 16, 1997 / Details: MAC SCIENCE DOUBLE MIRROR |
Radiation | Monochromator: 0.15 MM NICKEL FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. obs: 10332 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 8.657 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.204 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 6.07 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.351 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GV5 Resolution: 1.45→12.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 731165.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.5097 Å2 / ksol: 0.550446 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→12.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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