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- PDB-1tfg: AN UNUSUAL FEATURE REVEALED BY THE CRYSTAL STRUCTURE AT 2.2 ANGST... -

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Basic information

Entry
Database: PDB / ID: 1tfg
TitleAN UNUSUAL FEATURE REVEALED BY THE CRYSTAL STRUCTURE AT 2.2 ANGSTROMS RESOLUTION OF HUMAN TRANSFORMING GROWTH FACTOR-BETA2
ComponentsTRANSFORMING GROWTH FACTOR, BETA 2
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


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 / ascending aorta morphogenesis / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / somatic stem cell division ...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 / ascending aorta morphogenesis / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / somatic stem cell division / atrial septum morphogenesis / heart valve morphogenesis / cardiac right ventricle morphogenesis / pericyte cell differentiation / regulation of transforming growth factor beta2 production / transforming growth factor beta complex / uterus development / positive regulation of heart contraction / pharyngeal arch artery morphogenesis / negative regulation of macrophage cytokine production / glial cell migration / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of stress-activated MAPK cascade / salivary gland morphogenesis / atrial septum primum morphogenesis / positive regulation of extracellular matrix disassembly / membranous septum morphogenesis / secondary palate development / positive regulation of integrin biosynthetic process / endocardial cushion fusion / hair follicle development / cranial skeletal system development / cardiac epithelial to mesenchymal transition / embryonic limb morphogenesis / signaling / eye development / TGFBR3 regulates TGF-beta signaling / embryonic digestive tract development / cell-cell junction organization / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / transforming growth factor beta receptor binding / negative regulation of Ras protein signal transduction / neural retina development / atrioventricular valve morphogenesis / ventricular trabecula myocardium morphogenesis / embryo development ending in birth or egg hatching / collagen fibril organization / outflow tract septum morphogenesis / hair follicle morphogenesis / endocardial cushion morphogenesis / face morphogenesis / odontogenesis / positive regulation of cell adhesion mediated by integrin / Molecules associated with elastic fibres / ventricular septum morphogenesis / neural tube closure / positive regulation of Notch signaling pathway / dopamine biosynthetic process / inner ear development / generation of neurons / hemopoiesis / TGF-beta receptor signaling activates SMADs / response to progesterone / positive regulation of epithelial cell migration / positive regulation of cell division / cardiac muscle cell proliferation / positive regulation of SMAD protein signal transduction / heart morphogenesis / neuron development / epithelial to mesenchymal transition / skeletal system development / transforming growth factor beta receptor signaling pathway / ECM proteoglycans / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / cell morphogenesis / neutrophil chemotaxis / kidney development / negative regulation of angiogenesis / epithelial cell differentiation / male gonad development / positive regulation of cell cycle / platelet alpha granule lumen / cytokine activity / positive regulation of protein secretion / wound healing / regulation of actin cytoskeleton organization / growth factor activity / response to wounding / negative regulation of cell growth / positive regulation of protein localization to nucleus / negative regulation of epithelial cell proliferation / positive regulation of miRNA transcription / positive regulation of immune response / heart development / positive regulation of neuron apoptotic process / Platelet degranulation / regulation of cell population proliferation
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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...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 / 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
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsGruetter, M. / Schlunegger, M.
Citation
Journal: Nature / Year: 1992
Title: An unusual feature revealed by the crystal structure at 2.2 A resolution of human transforming growth factor-beta 2.
Authors: Schlunegger, M.P. / Grutter, M.G.
#1: Journal: FEBS Lett. / Year: 1992
Title: Crystallization and Preliminary X-Ray Analysis of Recombinant Human Transforming Growth Factor Beta2
Authors: Schlunegger, M.P. / Cerletti, N. / Cox, D.A. / Mcmaster, G.K. / Schmitz, A. / Gruetter, M.G.
#2: Journal: Science / Year: 1992
Title: Crystal Structure of Transforming Growth Factor-Beta2: An Unusual Fold for the Superfamily
Authors: Daopin, S. / Piez, K.A. / Ogawa, Y. / Davies, D.R.
History
DepositionNov 17, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)12,7331
Polymers12,7331
Non-polymers00
Water1,51384
1
A: TRANSFORMING GROWTH FACTOR, BETA 2

A: TRANSFORMING GROWTH FACTOR, BETA 2


Theoretical massNumber of molelcules
Total (without water)25,4652
Polymers25,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2550 Å2
ΔGint-28 kcal/mol
Surface area11680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.600, 60.600, 75.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUE 36 IS A CIS PROLINE.

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Components

#1: Protein TRANSFORMING GROWTH FACTOR, BETA 2


Mass: 12732.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61812
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMsodium acetate1drop
30.1 Msodium acetate1reservoir
425-35 %(w/v)PEG4001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 14995 / Rmerge(I) obs: 0.106

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.95→8 Å / Rfactor Rwork: 0.194 / Rfactor obs: 0.194
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 84 974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.97
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 8 Å / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.97

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