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- PDB-2qcw: Crystal Structure of Bone Morphogenetic Protein-6 (BMP-6) -

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Basic information

Entry
Database: PDB / ID: 2qcw
TitleCrystal Structure of Bone Morphogenetic Protein-6 (BMP-6)
ComponentsBone morphogenetic protein 6
KeywordsSIGNALING PROTEIN / BMP / TGF-beta
Function / homology
Function and homology information


positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / enzyme activator complex / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / type B pancreatic cell development / BMP receptor binding / eye development / endochondral ossification ...positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / enzyme activator complex / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / type B pancreatic cell development / BMP receptor binding / eye development / endochondral ossification / cellular response to BMP stimulus / male genitalia development / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of vascular permeability / positive regulation of lipopolysaccharide-mediated signaling pathway / cartilage development / positive regulation of intracellular signal transduction / response to magnesium ion / positive regulation of SMAD protein signal transduction / response to retinoic acid / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / response to glucocorticoid / cytokine activity / positive regulation of epithelial cell proliferation / response to activity / cellular response to iron ion / skeletal system development / positive regulation of protein secretion / growth factor activity / kidney development / cellular response to mechanical stimulus / bone development / multicellular organismal-level iron ion homeostasis / neuron differentiation / osteoblast differentiation / 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
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, 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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsAllendorph, G.P.
CitationJournal: Biochemistry / Year: 2007
Title: BMP-3 and BMP-6 Structures Illuminate the Nature of Binding Specificity with Receptors.
Authors: Allendorph, G.P. / Isaacs, M.J. / Kawakami, Y. / Belmonte, J.C. / Choe, S.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)29,7842
Polymers29,7842
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-25 kcal/mol
Surface area12140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.446, 97.446, 87.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biologically active unit is the dimer which is founf in the asymmetric unit.

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Components

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


Mass: 14891.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP6 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22004
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% 2-methyl-2,4-pentanediol (MPD), 0.2 M Tri-Na Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2006
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→42.5 Å / Num. obs: 16679 / % possible obs: 93 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.6
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.437 / Num. unique all: 1092 / % possible all: 57.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BMP-7 ligand monomer taken from PDB entry 1lxi

1lxi


Resolution: 2.49→42.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.153 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27589 808 5.1 %RANDOM
Rwork0.23285 ---
obs0.23486 15112 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.308 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0.8 Å20 Å2
2---1.59 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.49→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 65 1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221713
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9412340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52424.35978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71315266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.308156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021308
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2693
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21135
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6791.51061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22521688
X-RAY DIFFRACTIONr_scbond_it1.413742
X-RAY DIFFRACTIONr_scangle_it2.2934.5652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 41 -
Rwork0.341 660 -
obs--56.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6321-4.1741-1.162717.1011.94982.1341-0.4032-0.1435-0.13341.79870.34760.0214-0.07720.02810.05560.03720.06440.0627-0.17850.0598-0.0653-46.72177.309913.2727
21.96983.33521.009118.9784.6612.8054-0.04710.3285-0.1595-0.06890.1114-0.40910.04570.1136-0.0642-0.1691-0.0249-0.0265-0.16150.0122-0.0756-46.4369-6.94112.1443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA29 - 10429 - 104
2X-RAY DIFFRACTION2BB29 - 10429 - 104

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