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- PDB-2r53: Crystal structure analysis of Bone Morphogenetic Protein-6 varian... -

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Basic information

Entry
Database: PDB / ID: 2r53
TitleCrystal structure analysis of Bone Morphogenetic Protein-6 variant B2 (B2-BMP-6)
ComponentsBone morphogenetic protein 6
KeywordsCYTOKINE / BMP6 / Vgr / 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 / eye development / type B pancreatic cell development / positive regulation of lipopolysaccharide-mediated signaling pathway / endochondral ossification ...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 / eye development / type B pancreatic cell development / positive regulation of lipopolysaccharide-mediated signaling pathway / endochondral ossification / male genitalia development / negative regulation of cell-cell adhesion mediated by cadherin / cellular response to BMP stimulus / positive regulation of vascular permeability / cartilage development / response to magnesium ion / positive regulation of SMAD protein signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to retinoic acid / response to glucocorticoid / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / positive regulation of epithelial cell proliferation / skeletal system development / response to activity / cytokine activity / positive regulation of protein secretion / kidney development / cellular response to iron ion / growth factor activity / bone development / neuron differentiation / multicellular organismal-level iron ion homeostasis / cellular response to mechanical stimulus / osteoblast differentiation / positive regulation of peptidyl-tyrosine phosphorylation / intracellular iron ion homeostasis / vesicle / 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
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 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B ...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 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMueller, T.D. / Sebald, W.
CitationJournal: 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
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Residues 375 to 410 of BMP-6 are replaced by MAQAKHKQEKRLK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein 6
B: Bone morphogenetic protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0486
Polymers26,5752
Non-polymers4734
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.780, 99.780, 86.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains the biological homodimer

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Components

#1: Protein Bone morphogenetic protein 6 / BMP-6


Mass: 13287.490 Da / Num. of mol.: 2 / Fragment: BMP-6 variant B2, mature part
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 25% 2-Methyl-2,4-pentandiol, 0.1M sodium citrate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9183 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2002 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 2.1→500 Å / Num. all: 29537 / Num. obs: 28518 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rsym value: 0.058 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 4397 / Rsym value: 0.282 / % possible all: 95.7

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMP

1bmp


Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1426 -random
Rwork0.259 ---
all0.264 29494 --
obs0.261 28518 96.7 %-
Displacement parametersBiso mean: 62.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 110 1810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.475
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_improper_angle_d0.883

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