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- PDB-4mpl: Crystal structure of BMP9 at 1.90 Angstrom -

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Basic information

Entry
Database: PDB / ID: 4mpl
TitleCrystal structure of BMP9 at 1.90 Angstrom
ComponentsGrowth/differentiation factor 2
KeywordsCYTOKINE / growth factor/cytokine
Function / homology
Function and homology information


positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / positive regulation of bicellular tight junction assembly / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / positive regulation of BMP signaling pathway / negative regulation of endothelial cell migration / cartilage development ...positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / positive regulation of bicellular tight junction assembly / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / positive regulation of BMP signaling pathway / negative regulation of endothelial cell migration / cartilage development / blood vessel morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of endothelial cell proliferation / negative regulation of DNA replication / positive regulation of Notch signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / vasculogenesis / BMP signaling pathway / positive regulation of endothelial cell proliferation / protein serine/threonine kinase activator activity / ossification / negative regulation of angiogenesis / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / osteoblast differentiation / positive regulation of angiogenesis / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region
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
Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLi, W. / Morrell, N.W. / Wei, Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Regulation of Bone Morphogenetic Protein 9 (BMP9) by Redox-dependent Proteolysis.
Authors: Wei, Z. / Salmon, R.M. / Upton, P.D. / Morrell, N.W. / Li, W.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Jun 2, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth/differentiation factor 2


Theoretical massNumber of molelcules
Total (without water)12,9321
Polymers12,9321
Non-polymers00
Water1,63991
1
A: Growth/differentiation factor 2

A: Growth/differentiation factor 2


Theoretical massNumber of molelcules
Total (without water)25,8642
Polymers25,8642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
Buried area2500 Å2
ΔGint-23 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.270, 71.270, 145.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-270-

HOH

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Components

#1: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12931.852 Da / Num. of mol.: 1 / Fragment: UNP residues 321-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP9, GDF2 / Plasmid: pCEP4 / Cell line (production host): Hek293 / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.12M magnesium nitrate, 12% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC / Detector: CCD / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→40.17 Å / Num. all: 15096 / Num. obs: 15096 / % possible obs: 99.3 % / Redundancy: 7.8 % / Biso Wilson estimate: 30.79 Å2 / Rsym value: 0.075 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.9-280.75210.752198.6
2-2.1280.4091.90.409199
2.12-2.2780.2473.10.247199
2.27-2.4580.1564.90.156199.4
2.45-2.697.90.1116.80.111199.5
2.69-37.80.0749.40.074199.7
3-3.477.70.05711.10.057199.7
3.47-4.257.40.05310.70.053199.9
4.25-6.016.90.04612.40.046199.7
6.01-40.176.90.03616.70.036198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.95 Å40.17 Å
Translation1.95 Å40.17 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.17 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 769 5.1 %
Rwork0.1987 --
obs0.2 15087 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5972 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 91 905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008864
X-RAY DIFFRACTIONf_angle_d1.181174
X-RAY DIFFRACTIONf_dihedral_angle_d12.95309
X-RAY DIFFRACTIONf_chiral_restr0.093129
X-RAY DIFFRACTIONf_plane_restr0.005149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04670.3091510.26672780X-RAY DIFFRACTION98
2.0467-2.25270.28081380.22882813X-RAY DIFFRACTION99
2.2527-2.57860.26151590.21012837X-RAY DIFFRACTION99
2.5786-3.24860.24361770.20122854X-RAY DIFFRACTION99
3.2486-40.17870.17841440.17993034X-RAY DIFFRACTION99

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