+Open data
-Basic information
Entry | Database: PDB / ID: 1buo | ||||||
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Title | BTB DOMAIN FROM PLZF | ||||||
Components | PROTEIN (PROMYELOCYTIC LEUKEMIA ZINC FINGER PROTEIN PLZF) | ||||||
Keywords | GENE REGULATION / PROTEIN-PROTEIN INTERACTION DOMAIN / TRANSCRIPTIONAL REPRESSOR / ZINC-FINGER PROTEIN / PROTEIN STRUCTURE / PROMYELOCYTIC LEUKEMIA | ||||||
Function / homology | Function and homology information male germ-line stem cell asymmetric division / type 2 angiotensin receptor binding / forelimb morphogenesis / positive regulation of cartilage development / negative regulation of myeloid cell differentiation / positive regulation of chondrocyte differentiation / mesonephros development / positive regulation of NK T cell differentiation / embryonic pattern specification / myeloid cell differentiation ...male germ-line stem cell asymmetric division / type 2 angiotensin receptor binding / forelimb morphogenesis / positive regulation of cartilage development / negative regulation of myeloid cell differentiation / positive regulation of chondrocyte differentiation / mesonephros development / positive regulation of NK T cell differentiation / embryonic pattern specification / myeloid cell differentiation / positive regulation of ossification / embryonic hindlimb morphogenesis / cartilage development / ossification involved in bone maturation / anterior/posterior pattern specification / embryonic digit morphogenesis / hemopoiesis / protein localization to nucleus / positive regulation of fat cell differentiation / transcription repressor complex / transcription corepressor binding / central nervous system development / male germ cell nucleus / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / protein ubiquitination / nuclear body / nuclear speck / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / identical protein binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Ahmad, K.F. / Engel, C.K. / Prive, G.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Crystal structure of the BTB domain from PLZF. Authors: Ahmad, K.F. / Engel, C.K. / Prive, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1buo.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1buo.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 1buo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1buo ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1buo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13927.039 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-32(A) / Cell line (production host): B834(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05516 |
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#2: 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: 4 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 0.15 M CACL2, 0.1 M HEPES (PH 7.5), 4% ISOPROPANOL, | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9638, 0.9790, 0.9793 | ||||||||||||
Detector | Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→20 Å / Num. obs: 18253 / % possible obs: 99.3 % / Redundancy: 11.2 % / Rsym value: 0.044 / Net I/σ(I): 11.2 | ||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.248 / % possible all: 96.7 | ||||||||||||
Reflection | *PLUS Num. measured all: 204897 / Rmerge(I) obs: 0.044 | ||||||||||||
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.248 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.212 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |