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Open data
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Basic information
Entry | Database: PDB / ID: 1puf | ||||||
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Title | Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA | ||||||
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![]() | Transcription/DNA / Homeodomian / Protein-DNA complex / Hox Hexapeptide / TALE homeodomain / Homeodomain interaction / Transcription-DNA COMPLEX | ||||||
Function / homology | ![]() urogenital system development / negative regulation of myeloid cell differentiation / embryonic skeletal system morphogenesis / natural killer cell differentiation / embryonic skeletal system development / proximal/distal pattern formation / Transcriptional regulation of pluripotent stem cells / sex differentiation / eye development / mammary gland development ...urogenital system development / negative regulation of myeloid cell differentiation / embryonic skeletal system morphogenesis / natural killer cell differentiation / embryonic skeletal system development / proximal/distal pattern formation / Transcriptional regulation of pluripotent stem cells / sex differentiation / eye development / mammary gland development / steroid biosynthetic process / definitive hemopoiesis / embryonic forelimb morphogenesis / endothelial cell activation / embryonic limb morphogenesis / embryonic hemopoiesis / anterior/posterior pattern specification / NOTCH3 Intracellular Domain Regulates Transcription / branching involved in ureteric bud morphogenesis / adrenal gland development / positive regulation of stem cell proliferation / uterus development / negative regulation of neuron differentiation / regulation of ossification / single fertilization / neuron development / embryonic organ development / spleen development / positive regulation of G2/M transition of mitotic cell cycle / transcription corepressor binding / thymus development / stem cell proliferation / transcription coregulator binding / animal organ morphogenesis / brain development / negative regulation of DNA-binding transcription factor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / male gonad development / G2/M transition of mitotic cell cycle / sequence-specific double-stranded DNA binding / regulation of gene expression / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Laronde-Leblanc, N.A. / Wolberger, C. | ||||||
![]() | ![]() Title: STRUCTURE OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA RECOGNITION ANTERIOR TO POSTERIOR Authors: LARONDE-LEBLANC, N.A. / Wolberger, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b72S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 6083.953 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6182.029 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 9646.336 Da / Num. of mol.: 1 / Fragment: residues 193-269 Source method: isolated from a genetically manipulated source Details: Homeodomain / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 8747.872 Da / Num. of mol.: 1 / Fragment: residues 233-305 Source method: isolated from a genetically manipulated source Details: Homeodomain / Source: (gene. exp.) ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / pH: 7.5 Details: PEG 4000, hepes, cobaltic hexamine, dithiothrietol, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2000 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 28839 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.9→20 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.26 / % possible all: 94.1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 95.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 94.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B72 Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1537852.39 / Data cutoff high rms absF: 1537852.39 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 48.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 9.5 % / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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