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- PDB-1bgf: STAT-4 N-DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1bgf
TitleSTAT-4 N-DOMAIN
ComponentsSTAT-4
KeywordsTRANSCRIPTION FACTOR / REGULATION / DNA-BINDING
Function / homology
Function and homology information


Interleukin-21 signaling / Interleukin-20 family signaling / Interleukin-12 signaling / Interleukin-23 signaling / Interleukin-35 Signalling / : / cell surface receptor signaling pathway via JAK-STAT / response to peptide hormone / defense response / cytokine-mediated signaling pathway ...Interleukin-21 signaling / Interleukin-20 family signaling / Interleukin-12 signaling / Interleukin-23 signaling / Interleukin-35 Signalling / : / cell surface receptor signaling pathway via JAK-STAT / response to peptide hormone / defense response / cytokine-mediated signaling pathway / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Signal transducer and activator of transcription 4 / STAT4, SH2 domain / Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain ...Signal transducer and activator of transcription 4 / STAT4, SH2 domain / Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Signal transducer and activator of transcription 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsVinkemeier, U. / Moarefi, I. / Darnell, J.E. / Kuriyan, J.
CitationJournal: Science / Year: 1998
Title: Structure of the amino-terminal protein interaction domain of STAT-4.
Authors: Vinkemeier, U. / Moarefi, I. / Darnell Jr., J.E. / Kuriyan, J.
History
DepositionMay 28, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAT-4


Theoretical massNumber of molelcules
Total (without water)14,5041
Polymers14,5041
Non-polymers00
Water2,900161
1
A: STAT-4

A: STAT-4


Theoretical massNumber of molelcules
Total (without water)29,0072
Polymers29,0072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Unit cell
Length a, b, c (Å)79.500, 79.500, 84.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

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Components

#1: Protein STAT-4


Mass: 14503.691 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42228
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirNaCH3COO
20.1 MTris-HCl1reservoir
317 %PEG40001reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.45 Å / Num. obs: 237647 / % possible obs: 96.4 % / Rsym value: 0.072 / Net I/σ(I): 19.6
Reflection
*PLUS
Num. obs: 27594 / Num. measured all: 237647 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 91.7 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3.01refinement
X-PLOR3phasing
RefinementHighest resolution: 1.45 Å / Cross valid method: FREE R
Rfactor% reflectionSelection details
Rfree0.216 5 %RANDOM
Rwork0.188 --
obs0.188 --
Refinement stepCycle: LAST / Highest resolution: 1.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 161 1179
Software
*PLUS
Version: 3.01 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 26655 / Num. reflection obs: 25285 / σ(F): 2 / Rfactor all: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.4

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