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Yorodumi- PDB-1sqn: Progesterone Receptor Ligand Binding Domain with bound Norethindrone -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sqn | ||||||
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Title | Progesterone Receptor Ligand Binding Domain with bound Norethindrone | ||||||
Components | progesterone receptor | ||||||
Keywords | HORMONE/GROWTH FACTOR RECEPTOR / progesterone receptor / nuclear receptor / steroid receptor / norethindrone / birth control / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / negative regulation of phosphorylation / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / negative regulation of phosphorylation / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / SUMOylation of intracellular receptors / G protein-coupled receptor activity / Nuclear Receptor transcription pathway / transcription coactivator binding / nuclear receptor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / chromatin / regulation of DNA-templated transcription / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å | ||||||
Authors | Williams, S.P. / Madauss, K.P. / Deng, J.-S. / Austin, R.J.H. / Lambert, M.H. / McLay, I. / Pritchard, J. / Short, S.A. / Stewart, E.L. / Uings, I.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Progesterone receptor ligand binding pocket flexibility: crystal structures of the norethindrone and mometasone furoate complexes Authors: Madauss, K.P. / Deng, J.-S. / Austin, R.J.H. / Lambert, M.H. / McLay, I. / Pritchard, J. / Short, S.A. / Stewart, E.L. / Uings, I.J. / Williams, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sqn.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sqn.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sqn_validation.pdf.gz | 956.3 KB | Display | wwPDB validaton report |
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Full document | 1sqn_full_validation.pdf.gz | 971.1 KB | Display | |
Data in XML | 1sqn_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 1sqn_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/1sqn ftp://data.pdbj.org/pub/pdb/validation_reports/sq/1sqn | HTTPS FTP |
-Related structure data
Related structure data | 1sr7C 1a28S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30134.275 Da / Num. of mol.: 2 / Fragment: residues 676-933, ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: GST fusion / Gene: HUMPGRR / Plasmid: GST-PR LBD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: P06401 #2: Chemical | #3: 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: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 1000, Li2SO4. hepes pH 6.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 22K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 15, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.451→20 Å / Num. all: 63827 / Num. obs: 54571 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A28 Resolution: 1.451→19.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.978 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.422 Å2
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Refinement step | Cycle: LAST / Resolution: 1.451→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.489 Å / Total num. of bins used: 20 /
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