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Yorodumi- PDB-2r52: Crystal structure analysis of Bone Morphogenetic Protein-6 (BMP-6) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r52 | ||||||
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Title | Crystal structure analysis of Bone Morphogenetic Protein-6 (BMP-6) | ||||||
Components | Bone morphogenetic protein 6 | ||||||
Keywords | CYTOKINE / BMP-6 / TGF-beta ligand / Chondrogenesis / Cleavage on pair of basic residues / Developmental protein / Differentiation / Glycoprotein / Growth factor / Osteogenesis / Secreted | ||||||
Function / homology | Function and homology information positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / BMP receptor binding / type B pancreatic cell development / eye development / positive regulation of lipopolysaccharide-mediated signaling pathway / male genitalia development ...positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / BMP receptor binding / type B pancreatic cell development / eye development / positive regulation of lipopolysaccharide-mediated signaling pathway / male genitalia development / cellular response to BMP stimulus / negative regulation of cell-cell adhesion mediated by cadherin / endochondral ossification / positive regulation of vascular permeability / cartilage development / positive regulation of SMAD protein signal transduction / response to magnesium ion / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of bone mineralization / response to retinoic acid / response to glucocorticoid / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / response to activity / kidney development / skeletal system development / cytokine activity / positive regulation of epithelial cell proliferation / positive regulation of protein secretion / growth factor activity / bone development / neuron differentiation / cellular response to iron ion / osteoblast differentiation / multicellular organismal-level iron ion homeostasis / cellular response to mechanical stimulus / positive regulation of peptidyl-tyrosine phosphorylation / vesicle / intracellular iron ion homeostasis / immune response / inflammatory response / protein heterodimerization activity / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mueller, T.D. / Sebald, W. / Saremba, S. | ||||||
Citation | Journal: Febs J. / Year: 2007 Title: Type I receptor binding of bone morphogenetic protein 6 is dependent on N-glycosylation of the ligand. Authors: Saremba, S. / Nickel, J. / Seher, A. / Kotzsch, A. / Sebald, W. / Mueller, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r52.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r52.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 2r52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r52 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r52 | HTTPS FTP |
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-Related structure data
Related structure data | 2r53C 1bmpS 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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Details | The asymmetric unit contains the biological homodimer |
-Components
#1: Protein | Mass: 16096.207 Da / Num. of mol.: 2 / Fragment: Mature part (residues 375-513) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMP6, VGR / Plasmid: pN25 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22004 #2: Chemical | ChemComp-IPA / #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: 3.64 Å3/Da / Density % sol: 66.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% 2-propanol, 0.1M sodium citrate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 16, 2001 / Details: Osmic Blue |
Radiation | Monochromator: multi-layer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→59.98 Å / Num. obs: 16706 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.051 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1637 / Rsym value: 0.397 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BMP BMP-7 Resolution: 2.5→59.98 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→59.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.69 Å
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