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Yorodumi- PDB-6mgm: Helix-Loop-helix motif of mouse DNA-binding protein inhibitor ID-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mgm | ||||||
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Title | Helix-Loop-helix motif of mouse DNA-binding protein inhibitor ID-1 | ||||||
Components | DNA-binding protein inhibitor ID-1 | ||||||
Keywords | DNA BINDING PROTEIN / Helix-loop-helix DNA-binding protein inhibitor | ||||||
Function / homology | Function and homology information regulation of vasculature development / negative regulation of endothelial cell differentiation / Oncogene Induced Senescence / lung vasculature development / negative regulation of dendrite morphogenesis / collagen metabolic process / positive regulation of actin filament bundle assembly / endothelial cell morphogenesis / endothelial cell apoptotic process / transcription regulator inhibitor activity ...regulation of vasculature development / negative regulation of endothelial cell differentiation / Oncogene Induced Senescence / lung vasculature development / negative regulation of dendrite morphogenesis / collagen metabolic process / positive regulation of actin filament bundle assembly / endothelial cell morphogenesis / endothelial cell apoptotic process / transcription regulator inhibitor activity / negative regulation of cold-induced thermogenesis / lung morphogenesis / proteasome binding / regulation of MAPK cascade / negative regulation of osteoblast differentiation / BMP signaling pathway / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / positive regulation of epithelial cell proliferation / circadian regulation of gene expression / protein destabilization / circadian rhythm / : / heart development / cell differentiation / protein dimerization activity / response to antibiotic / negative regulation of gene expression / centrosome / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of gene expression / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.791 Å | ||||||
Authors | Benezra, R. / Pavletich, N.P. / Goldgur, Y. / Gall, A.-L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2019 Title: A Small-Molecule Pan-Id Antagonist Inhibits Pathologic Ocular Neovascularization. Authors: Wojnarowicz, P.M. / Lima E Silva, R. / Ohnaka, M. / Lee, S.B. / Chin, Y. / Kulukian, A. / Chang, S.H. / Desai, B. / Garcia Escolano, M. / Shah, R. / Garcia-Cao, M. / Xu, S. / Kadam, R. / ...Authors: Wojnarowicz, P.M. / Lima E Silva, R. / Ohnaka, M. / Lee, S.B. / Chin, Y. / Kulukian, A. / Chang, S.H. / Desai, B. / Garcia Escolano, M. / Shah, R. / Garcia-Cao, M. / Xu, S. / Kadam, R. / Goldgur, Y. / Miller, M.A. / Ouerfelli, O. / Yang, G. / Arakawa, T. / Albanese, S.K. / Garland, W.A. / Stoller, G. / Chaudhary, J. / Norton, L. / Soni, R.K. / Philip, J. / Hendrickson, R.C. / Iavarone, A. / Dannenberg, A.J. / Chodera, J.D. / Pavletich, N. / Lasorella, A. / Campochiaro, P.A. / Benezra, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mgm.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mgm.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 6mgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgm ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgm | HTTPS FTP |
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-Related structure data
Related structure data | 6mgnC 6u2uC 1mdyS 5t9o S: Starting model for refinement C: citing same article (ref.) |
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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: 6264.212 Da / Num. of mol.: 2 / Fragment: unp residues 52-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Id1, Id, Id-1, Idb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20067 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium citrate (pH 6.5), 0.2 M magnesium acetate, 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 8782 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rpim(I) all: 0.044 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Rpim(I) all: 0.231 / Rsym value: 0.376 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MDY Resolution: 1.791→21.437 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.791→21.437 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.7165 Å / Origin y: -0.6715 Å / Origin z: 14.0714 Å
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Refinement TLS group | Selection details: all |