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- PDB-5tx2: Miniature TGF-beta2 3-mutant monomer -

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Basic information

Entry
Database: PDB / ID: 5tx2
TitleMiniature TGF-beta2 3-mutant monomer
ComponentsTransforming growth factor beta-2
KeywordsCYTOKINE / Growth factor
Function / homology
Function and homology information


positive regulation of activation-induced cell death of T cells / transforming growth factor beta complex / positive regulation of GTP binding / negative regulation of alkaline phosphatase activity / Molecules associated with elastic fibres / : / regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation ...positive regulation of activation-induced cell death of T cells / transforming growth factor beta complex / positive regulation of GTP binding / negative regulation of alkaline phosphatase activity / Molecules associated with elastic fibres / : / regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / : / TGF-beta receptor signaling activates SMADs / ascending aorta morphogenesis / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / : / embryonic neurocranium morphogenesis / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / positive regulation of extracellular matrix disassembly / transforming growth factor beta ligand-receptor complex / atrial septum morphogenesis / positive regulation of heart contraction / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / negative regulation of keratinocyte differentiation / activation-induced cell death of T cells / secondary palate development / cardiac left ventricle morphogenesis / positive regulation of stress-activated MAPK cascade / glial cell migration / cell death / somatic stem cell division / heart valve morphogenesis / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / negative regulation of cartilage development / Platelet degranulation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / pericyte cell differentiation / neural retina development / neuron fate commitment / eye development / cranial skeletal system development / regulation of extracellular matrix organization / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / outflow tract septum morphogenesis / negative regulation of Ras protein signal transduction / negative regulation of immune response / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / SMAD protein signal transduction / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of release of sequestered calcium ion into cytosol / collagen fibril organization / embryonic limb morphogenesis / face morphogenesis / positive regulation of cell adhesion mediated by integrin / dopamine biosynthetic process / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / hair follicle morphogenesis / cartilage condensation / ventricular septum morphogenesis / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / blood vessel development / outflow tract morphogenesis / activation of protein kinase activity / inner ear development / uterus development / hemopoiesis / positive regulation of cell division / basement membrane / hair follicle development / neuron development / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / blood vessel remodeling / BMP signaling pathway / positive regulation of cell cycle / salivary gland morphogenesis / heart morphogenesis / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / extracellular matrix organization / negative regulation of angiogenesis / extracellular matrix / neutrophil chemotaxis / transforming growth factor beta receptor signaling pathway
Similarity search - Function
Transforming growth factor beta-2 proprotein / Transforming growth factor-beta / 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 ...Transforming growth factor beta-2 proprotein / Transforming growth factor-beta / 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 cytokine
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTaylor, A.B. / Kim, S.K. / Hart, P.J. / Hinck, A.P.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: An engineered transforming growth factor beta (TGF-beta ) monomer that functions as a dominant negative to block TGF-beta signaling.
Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / ...Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / Barnes, C.O. / Sulea, T. / Calero, G. / Hart, P.J. / Hart, M.J. / Demeler, B. / Hinck, A.P.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Oct 4, 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: Transforming growth factor beta-2
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)21,2072
Polymers21,2072
Non-polymers00
Water1,928107
1
A: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,6031
Polymers10,6031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,6031
Polymers10,6031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.459, 33.355, 54.131
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

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Components

#1: Protein Transforming growth factor beta-2 / / TGF-beta-2


Mass: 10603.290 Da / Num. of mol.: 2 / Fragment: UNP residues 303-414 / Mutation: L51R,A74K,C77S
Source method: isolated from a genetically manipulated source
Details: Residues 52-71 were deleted. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tgfb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27090
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→51.01 Å / Num. obs: 15033 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TGI

2tgi


Resolution: 1.82→51.01 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 27.94
RfactorNum. reflection% reflection
Rfree0.2519 1503 10 %
Rwork0.2091 --
obs0.2133 15027 98.15 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 1.82→51.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 107 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121508
X-RAY DIFFRACTIONf_angle_d1.032050
X-RAY DIFFRACTIONf_dihedral_angle_d12.902582
X-RAY DIFFRACTIONf_chiral_restr0.064214
X-RAY DIFFRACTIONf_plane_restr0.007262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.87870.35691350.30221216X-RAY DIFFRACTION98
1.8787-1.94590.29411360.25651229X-RAY DIFFRACTION99
1.9459-2.02380.32051340.23181211X-RAY DIFFRACTION99
2.0238-2.11590.32951370.21471228X-RAY DIFFRACTION99
2.1159-2.22750.27631370.22191232X-RAY DIFFRACTION99
2.2275-2.3670.32521370.22421227X-RAY DIFFRACTION98
2.367-2.54980.28651350.21531218X-RAY DIFFRACTION99
2.5498-2.80640.28451370.23221237X-RAY DIFFRACTION99
2.8064-3.21240.25071380.21241237X-RAY DIFFRACTION98
3.2124-4.0470.21011350.19371219X-RAY DIFFRACTION96
4.047-51.03040.21021420.18631270X-RAY DIFFRACTION97

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