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- PDB-1reu: Structure of the bone morphogenetic protein 2 mutant L51P -

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Basic information

Entry
Database: PDB / ID: 1reu
TitleStructure of the bone morphogenetic protein 2 mutant L51P
Componentsbone morphogenetic protein 2
KeywordsHORMONE/GROWTH FACTOR / TGF-beta fold / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / mesenchymal cell proliferation involved in ureteric bud development / enzyme activator complex / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / negative regulation of insulin-like growth factor receptor signaling pathway / ameloblast differentiation / aortic valve development / pericardium development / telencephalon regionalization / heart induction / positive regulation of cartilage development / positive regulation of odontogenesis / positive regulation of peroxisome proliferator activated receptor signaling pathway / BMP receptor complex / proteoglycan metabolic process / co-receptor binding / lung vasculature development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / telencephalon development / BMP receptor binding / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / phosphatase activator activity / Transcriptional regulation by RUNX2 / endocardial cushion formation / positive regulation of astrocyte differentiation / cellular response to BMP stimulus / Signaling by BMP / cardiac muscle cell differentiation / astrocyte differentiation / cardiac muscle tissue morphogenesis / positive regulation of ossification / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / branching involved in ureteric bud morphogenesis / positive regulation of osteoblast proliferation / negative regulation of fat cell differentiation / bone mineralization / odontogenesis of dentin-containing tooth / negative regulation of cell cycle / inner ear development / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / cell fate commitment / positive regulation of Wnt signaling pathway / chondrocyte differentiation / positive regulation of fat cell differentiation / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / osteoclast differentiation / animal organ morphogenesis / protein serine/threonine kinase activator activity / cytokine activity / skeletal system development / response to bacterium / growth factor activity / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of canonical Wnt signaling pathway / bone development / protein destabilization / positive regulation of miRNA transcription / positive regulation of protein phosphorylation / Regulation of RUNX2 expression and activity / osteoblast differentiation / cell-cell signaling / heart development / in utero embryonic development / transcription by RNA polymerase II / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / cilium / positive regulation of cell migration / positive regulation of apoptotic process / inflammatory response / signaling receptor binding / negative regulation of cell population proliferation
Similarity search - Function
: / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal ...: / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKeller, S. / Nickel, J. / Zhang, J.-L. / Sebald, W. / Mueller, T.D.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Molecular recognition of BMP-2 and BMP receptor IA.
Authors: Keller, S. / Nickel, J. / Zhang, J.L. / Sebald, W. / Mueller, T.D.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of human bone morphogenetic protein-2 at 2.7 A resolution
Authors: Scheufler, C. / Sebald, W. / Huelsmeyer, M.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the BMP-2-BRIA ectodomain complex
Authors: Kirsch, T. / Sebald, W. / Dreyer, M.K.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7343
Polymers11,4981
Non-polymers2362
Water23413
1
A: bone morphogenetic protein 2
hetero molecules

A: bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4696
Polymers22,9962
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area3640 Å2
ΔGint-64 kcal/mol
Surface area11210 Å2
MethodPISA, PQS
2
A: bone morphogenetic protein 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)70,40618
Polymers68,9886
Non-polymers1,41812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area9410 Å2
ΔGint-163 kcal/mol
Surface area35140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.292, 94.292, 102.882
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
DetailsThe biological assembly is a dimer generated by the two fold axis (disulfide bonded homodimer): 2/3+x-y, 1/3-y, 1/3-z

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Components

#1: Protein bone morphogenetic protein 2


Mass: 11498.064 Da / Num. of mol.: 1 / Fragment: mature part / Mutation: L51P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pN25c109 / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: lithium sulfate, tert-butanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2003 / Details: Osmic ConfocalBlue
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→19.76 Å / Num. all: 5624 / Num. obs: 5624 / % possible obs: 93.5 % / Observed criterion σ(I): 1.2 / Redundancy: 3.4 % / Biso Wilson estimate: 101.2 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.65→2.82 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.293 / % possible all: 72.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNS1.1refinement
CCP4(SCALA)data scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BMP

3bmp


Resolution: 2.65→19.76 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1489344.52 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 259 5.3 %RANDOM
Rwork0.215 ---
all0.216 5624 --
obs0.2151 4918 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4107 Å2 / ksol: 0.310865 e/Å3
Displacement parametersBiso mean: 64.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å24.25 Å20 Å2
2--4.21 Å20 Å2
3----8.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 16 13 833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.331
X-RAY DIFFRACTIONc_mcangle_it2.461.5
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 35 5.6 %
Rwork0.332 587 -
obs-377 72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD_XPLOR_PAR.PROMPD_XPLOR_TOP.PAR

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