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- PDB-1tgk: HUMAN TRANSFORMING GROWTH FACTOR BETA 3, CRYSTALLIZED FROM PEG 4000 -

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Basic information

Entry
Database: PDB / ID: 1tgk
TitleHUMAN TRANSFORMING GROWTH FACTOR BETA 3, CRYSTALLIZED FROM PEG 4000
ComponentsTRANSFORMING GROWTH FACTOR BETA 3
KeywordsGROWTH FACTOR / MITOGEN / GLYCOPROTEIN
Function / homology
Function and homology information


uterine wall breakdown / detection of hypoxia / type III transforming growth factor beta receptor binding / secondary palate development / negative regulation of macrophage cytokine production / positive regulation of tight junction disassembly / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / mammary gland development / cell-cell junction organization ...uterine wall breakdown / detection of hypoxia / type III transforming growth factor beta receptor binding / secondary palate development / negative regulation of macrophage cytokine production / positive regulation of tight junction disassembly / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / mammary gland development / cell-cell junction organization / transforming growth factor beta binding / face morphogenesis / odontogenesis / positive regulation of filopodium assembly / Molecules associated with elastic fibres / lung alveolus development / TGF-beta receptor signaling activates SMADs / positive regulation of collagen biosynthetic process / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell division / positive regulation of SMAD protein signal transduction / ECM proteoglycans / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / positive regulation of stress fiber assembly / transforming growth factor beta receptor signaling pathway / response to progesterone / platelet alpha granule lumen / cytokine activity / positive regulation of protein secretion / growth factor activity / Platelet degranulation / regulation of cell population proliferation / : / in utero embryonic development / negative regulation of neuron apoptotic process / response to hypoxia / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Transforming growth factor beta-3 / 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-3 / 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-3 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsMittl, P.R.E. / Priestle, J.P. / Gruetter, M.G.
Citation
Journal: Protein Sci. / Year: 1996
Title: The crystal structure of TGF-beta 3 and comparison to TGF-beta 2: implications for receptor binding.
Authors: Mittl, P.R. / Priestle, J.P. / Cox, D.A. / McMaster, G. / Cerletti, N. / Grutter, M.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Crystal Structure of Human Transforming Growth Factor Beta 2 at 1.95 A Resolution
Authors: Schlunegger, M.P. / Grutter, M.G.
History
DepositionJul 10, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
Revision 1.4Nov 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 3


Theoretical massNumber of molelcules
Total (without water)12,7351
Polymers12,7351
Non-polymers00
Water00
1
A: TRANSFORMING GROWTH FACTOR BETA 3

A: TRANSFORMING GROWTH FACTOR BETA 3


Theoretical massNumber of molelcules
Total (without water)25,4692
Polymers25,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+3/21
Buried area2420 Å2
ΔGint-27 kcal/mol
Surface area11530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.800, 77.800, 143.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TRANSFORMING GROWTH FACTOR BETA 3 / TGF-BETA3


Mass: 12734.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: STRAIN DEPOSITED AT DEUTSCHE SAMMLUNG VON MIKROORGANISMEN, MASCHENRODER WEG 1B, 3300 BRAUNSCHWEIG, GERMANY, ACCESSION NUMBER DSM 5658
Gene: HTGF-BETA3 / Plasmid: PPLMU / Gene (production host): HTGF-BETA3 / Production host: Escherichia coli (E. coli) / Strain (production host): LC137 / References: UniProt: P10600
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: 5.08 Å3/Da / Density % sol: 74.94 %
Crystal growDetails: PEG 4000
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 8.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5-3 mg/mlprotein1drop
25 mMacetic acid1drop
315 %(w/v)PEG40001drop
4100 mMmagnesium chloride1drop
550 mMTris-HCl1droppH8.4
630 %(w/v)PEG40001reservoir
7200 mMmagnesium chloride1reservoir
8100 mMTris-HCl1reservoirpH8.4

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 23, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 4232 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.132
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 9999 Å
Reflection shell
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.36 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
MADNESdata collection
ROTAVATA-AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementResolution: 3.3→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.228 -
obs0.228 4052
Displacement parametersBiso mean: 40.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 0 890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.92
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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