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Yorodumi- PDB-2hlr: Crystal Structure of the Extracellular Domain of the Type II BMP ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hlr | ||||||
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Title | Crystal Structure of the Extracellular Domain of the Type II BMP Receptor | ||||||
Components | Bone morphogenetic protein receptor type-2 | ||||||
Keywords | TRANSFERASE / three-finger toxin / bmp receptor / tgf-beta | ||||||
Function / homology | Function and homology information transmembrane receptor protein serine/threonine kinase activity / membrane => GO:0016020 / ATP binding Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | ||||||
Authors | Mace, P.D. / Cutfield, J.F. / Cutfield, S.M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2006 Title: High resolution structures of the bone morphogenetic protein type II receptor in two crystal forms: Implications for ligand binding Authors: Mace, P.D. / Cutfield, J.F. / Cutfield, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hlr.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hlr.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/2hlr ftp://data.pdbj.org/pub/pdb/validation_reports/hl/2hlr | HTTPS FTP |
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-Related 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: 11146.431 Da / Num. of mol.: 1 / Fragment: residues 32-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Gene: BMPRII / Plasmid: pet21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q91WY9, receptor protein serine/threonine kinase |
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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: 1.67 Å3/Da / Density % sol: 26.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Na Citrate, 25% PEG2000 MME, 0.8M Sodium Formate, pH 6.0, vapor diffusion, hanging drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→24.29 Å / Num. obs: 23947 / % possible obs: 98.1 % / Redundancy: 29.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.2→1.232 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 13.6 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→24.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.48 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.349 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→24.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.232 Å / Total num. of bins used: 20
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