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- PDB-1gvj: ETS-1 DNA BINDING AND AUTOINHIBITORY DOMAINS -

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Basic information

Entry
Database: PDB / ID: 1gvj
TitleETS-1 DNA BINDING AND AUTOINHIBITORY DOMAINS
ComponentsC-ETS-1 PROTEIN
KeywordsTRANSCRIPTION / ETS-1 / AUTOINHIBITION / ETS DOMAIN
Function / homology
Function and homology information


PML body organization / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration / transcription corepressor binding / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / cell motility ...PML body organization / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration / transcription corepressor binding / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / cell motility / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family ...Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsTahirov, T.H. / Ogata, K.
CitationJournal: To be Published
Title: Crystal Structure of C-Ets-1 DNA-Binding and Autoinhibitory Domains
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Ogata, K.
History
DepositionFeb 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-ETS-1 PROTEIN
B: C-ETS-1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,0152
Polymers34,0152
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.475, 42.842, 49.771
Angle α, β, γ (deg.)115.25, 97.30, 102.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.28687, -0.95735, -0.03434), (-0.95716, -0.28792, 0.03066), (-0.03924, 0.02408, -0.99894)
Vector: 22.0222, 27.59034, 49.1285)

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Components

#1: Protein C-ETS-1 PROTEIN / P54


Mass: 17007.449 Da / Num. of mol.: 2 / Fragment: RESIDUES 297-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14921
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 297 K / pH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 30% W/V PEG 4000, 0.1 M SODIUM CITRATE PH 5.6, PROTEIN CONCENTRATION 15 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K, FOR CRYOPROTECTION 10% OF PEG 400 WAS ADDED.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU IMAGE PLATE RAXIS V / Detector: IMAGE PLATE / Date: Jun 17, 2001 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 40937 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 3.103 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.648
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.021 / % possible all: 87.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AWC

1awc


Resolution: 1.53→28.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1125447.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2010 5 %RANDOM
Rwork0.208 ---
obs0.208 40277 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0866 Å2 / ksol: 0.372983 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å2-2.39 Å21.35 Å2
2---0.94 Å2-0.7 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-20 Å
Luzzati sigma a0.22 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.53→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 0 293 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.012.5
LS refinement shellResolution: 1.53→1.63 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 318 5.1 %
Rwork0.328 5884 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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