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- PDB-1tgj: HUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE -

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Basic information

Entry
Database: PDB / ID: 1tgj
TitleHUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE
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
1,4-DIETHYLENE DIOXIDE / Transforming growth factor beta-3 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2 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 9, 1996Processing site: BNL
Revision 1.0Jan 11, 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 2.0Apr 3, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSFORMING GROWTH FACTOR-BETA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8232
Polymers12,7351
Non-polymers881
Water1,38777
1
A: TRANSFORMING GROWTH FACTOR-BETA 3
hetero molecules

A: TRANSFORMING GROWTH FACTOR-BETA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6454
Polymers25,4692
Non-polymers1762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2610 Å2
ΔGint-22 kcal/mol
Surface area12200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.300, 49.300, 78.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-155-

HOH

21A-190-

HOH

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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
Details: ONE DIOXANE MOLECULE BOUND / Source: (gene. exp.) Homo sapiens (human)
Description: STRAIN DEPOSITED AT DEUTSCHE SAMMLUNG VON MIKROORGANISMEN, MASCHENRODER WEG 1B, 3300 BRAUNSCHWEIG, GERMANY, ACCESSION NUMBER IS 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
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE PROTEIN WAS CRYSTALLIZED FROM A SOLUTION CONTAINING 15 % DIOXANE. ONE DIOXANE MOLECULE IS BOUND ...THE PROTEIN WAS CRYSTALLIZED FROM A SOLUTION CONTAINING 15 % DIOXANE. ONE DIOXANE MOLECULE IS BOUND IN THE STRUCTURE.

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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: 2.25 Å3/Da / Density % sol: 43.37 %
Crystal growpH: 5 / Details: 15% (V/V) DIOXANE, 100 MM SODIUM ACETATE, PH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13-6 mg/mlprotein1drop
210 mMacetic acid1drop
315 %(v/v)dioxane1reservoir
4100 mMsodium acetate1reservoirpH5.0
51

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 16, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 6323 / % possible obs: 76 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.353 / % possible all: 37.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å
Reflection shell
*PLUS
% possible obs: 37.4 %

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Processing

Software
NameVersionClassification
MADNESdata collection
ROTAVATAdata reduction
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: TGF-BETA2 (SCHLUNEGGER & GRUETTER)

Resolution: 2→7 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.175 --
obs0.175 6127 76 %
Displacement parametersBiso mean: 29.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 6 77 973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.07
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_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
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
LS refinement shellResolution: 2→2.1 Å / % reflection obs: 37.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.89
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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