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- PDB-2hlq: Crystal Structure of the Extracellular Domain of the Type II BMP ... -

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Basic information

Entry
Database: PDB / ID: 2hlq
TitleCrystal Structure of the Extracellular Domain of the Type II BMP Receptor
ComponentsBone morphogenetic protein receptor type-2
KeywordsTRANSFERASE / receptor / serine kinase / three-finger toxin / ligand binding domain
Function / homology
Function and homology information


: / semi-lunar valve development / : / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / pulmonary valve development / tricuspid valve morphogenesis / chondrocyte development ...: / semi-lunar valve development / : / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / pulmonary valve development / tricuspid valve morphogenesis / chondrocyte development / lung vasculature development / lymphangiogenesis / negative regulation of cell proliferation involved in heart valve morphogenesis / venous blood vessel development / pharyngeal arch artery morphogenesis / aortic valve development / BMP binding / proteoglycan biosynthetic process / maternal placenta development / negative regulation of muscle cell differentiation / atrial septum morphogenesis / endocardial cushion development / positive regulation of cartilage development / endochondral bone morphogenesis / transforming growth factor beta receptor activity / retina vasculature development in camera-type eye / mitral valve morphogenesis / BMP receptor activity / positive regulation of axon extension involved in axon guidance / artery development / receptor protein serine/threonine kinase / Signaling by BMP / cellular response to BMP stimulus / outflow tract septum morphogenesis / positive regulation of BMP signaling pathway / endothelial cell apoptotic process / negative regulation of DNA biosynthetic process / positive regulation of ossification / negative regulation of systemic arterial blood pressure / vasculature development / endothelial cell proliferation / limb development / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / negative regulation of vasoconstriction / lung alveolus development / ventricular septum morphogenesis / positive regulation of epithelial cell migration / blood vessel development / outflow tract morphogenesis / growth factor binding / plasma membrane => GO:0005886 / positive regulation of SMAD protein signal transduction / mesoderm formation / blood vessel remodeling / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of bone mineralization / clathrin-coated pit / protein tyrosine kinase binding / cellular response to starvation / positive regulation of endothelial cell proliferation / basal plasma membrane / positive regulation of endothelial cell migration / caveola / negative regulation of smooth muscle cell proliferation / adherens junction / brain development / negative regulation of cell growth / cellular response to growth factor stimulus / osteoblast differentiation / regulation of cell population proliferation / postsynaptic density / receptor complex / cadherin binding / apical plasma membrane / axon / phosphorylation / protein phosphorylation / protein serine/threonine kinase activity / dendrite / neuronal cell body / positive regulation of gene expression / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Bone morphogenetic protein receptor type-2 / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein kinase domain / Protein kinase, ATP binding site ...Bone morphogenetic protein receptor type-2 / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein receptor type-2 / Bone morphogenetic protein receptor type-2
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMace, P.D. / Cutfield, J.F. / Cutfield, S.M.
CitationJournal: 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
DepositionJul 9, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)11,1461
Polymers11,1461
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.588, 45.078, 48.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bone morphogenetic protein receptor type-2 / Bone morphogenetic receptor type II / BMPRII


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: Q4ZG08, UniProt: Q13873*PLUS, receptor protein serine/threonine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Na Citrate, 15% PEG1500, 0.2M Mg acetate, pH 6.0, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 9.7 / Number: 52347 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / D res high: 1.45 Å / D res low: 27.932 Å / Num. obs: 13746 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
4.5932.9295.910.0280.0283.5
3.244.5997.510.0250.0253.5
2.653.2498.910.0340.0343.6
2.292.6599.310.0420.0423.8
2.052.2999.110.0520.0523.8
1.872.0599.210.0750.0753.9
1.731.8797.810.1190.1193.9
1.621.7398.310.1970.1973.9
1.531.6297.210.2680.2684
1.451.5387.110.3780.3783.7
ReflectionResolution: 1.45→27.932 Å / Num. obs: 13746 / % possible obs: 96.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.533.70.3781.1641117440.37887.1
1.53-1.6240.2682.7748118890.26897.2
1.62-1.733.90.1973.8702317800.19798.3
1.73-1.873.90.1196.1659816790.11997.8
1.87-2.053.90.0758.4597215440.07599.2
2.05-2.293.80.05211.4546014190.05299.1
2.29-2.653.80.04215.7480012700.04299.3
2.65-3.243.60.03415.5394810870.03498.9
3.24-4.593.50.02522.429158340.02597.5
4.59-32.923.50.02819.917395000.02895.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.63 Å22.54 Å
Translation1.63 Å22.54 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HLR

2hlr


Resolution: 1.45→22.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.734 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23159 707 5.2 %RANDOM
Rwork0.19017 ---
obs0.1923 13003 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.45→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 0 92 904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021842
X-RAY DIFFRACTIONr_bond_other_d0.0040.02558
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9271155
X-RAY DIFFRACTIONr_angle_other_deg0.8833.0061366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85825.12241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34215136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.71153
X-RAY DIFFRACTIONr_chiral_restr0.0920.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02169
X-RAY DIFFRACTIONr_nbd_refined0.210.2176
X-RAY DIFFRACTIONr_nbd_other0.2030.2541
X-RAY DIFFRACTIONr_nbtor_refined0.180.2400
X-RAY DIFFRACTIONr_nbtor_other0.0830.2447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4111.5690
X-RAY DIFFRACTIONr_mcbond_other0.3451.5214
X-RAY DIFFRACTIONr_mcangle_it1.732847
X-RAY DIFFRACTIONr_scbond_it2.2593417
X-RAY DIFFRACTIONr_scangle_it2.794.5304
X-RAY DIFFRACTIONr_rigid_bond_restr1.54431847
X-RAY DIFFRACTIONr_sphericity_free4.046393
X-RAY DIFFRACTIONr_sphericity_bonded1.79131370
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 33 -
Rwork0.194 756 -
obs--77.13 %

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