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- PDB-5ybc: X-ray structure of native ETS-domain domain of Ergp55 -

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Basic information

Entry
Database: PDB / ID: 5ybc
TitleX-ray structure of native ETS-domain domain of Ergp55
ComponentsTranscriptional regulator ERGERG (gene)
KeywordsSTRUCTURAL PROTEIN / ETS transcription factor / Ergp55
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / signal transduction ...sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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. ...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
Transcriptional regulator ERG
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSaxena, A.K. / Gangwar, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & TechnologySR/SO/HS-05/2009 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence
Authors: Sharma, R. / Gangwar, S.P. / Saxena, A.K.
History
DepositionSep 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Transcriptional regulator ERG
A: Transcriptional regulator ERG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9793
Polymers21,8872
Non-polymers921
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint3 kcal/mol
Surface area11230 Å2
Unit cell
Length a, b, c (Å)64.565, 64.565, 128.305
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain C and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain C and segid CC0

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Components

#1: Protein Transcriptional regulator ERG / ERG (gene) / Transforming protein ERG


Mass: 10943.370 Da / Num. of mol.: 2 / Fragment: ETS domain, UNP residues 317-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERG / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P11308
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.05 Å3/Da / Density % sol: 59.73 % / Description: rectangular bypyramid
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20%(w/v) PEG400, 130mM NaCl, 60mM MgCl2, 100mM sodium citrate pH 5.6
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2013 / Details: Grazing angle 2.8 mrad
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9971 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 27.5 % / Biso Wilson estimate: 60.86 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.985 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
2.5-2.5425.74870.665199.4
2.54-2.5926.94820.661199.60.989
2.59-2.6427.94700.676199.60.924
2.64-2.6927.75010.684199.80.807
2.69-2.7528.74650.693199.80.7
2.75-2.8228.35030.713199.80.605
2.82-2.8928.64790.732199.80.458
2.89-2.9628.64860.746199.80.346
2.96-3.0528.34940.766199.80.271
3.05-3.1528.54830.785199.60.186
3.15-3.2628.44980.822199.80.151
3.26-3.3928.54950.851199.60.102
3.39-3.55284850.90111000.08
3.55-3.7328.14971.16611000.071
3.73-3.9727.75070.99711000.056
3.97-4.2727.55051.14711000.044
4.27-4.727.25051.478199.40.042
4.7-5.3826.65251.956199.60.046
5.38-6.7826.45241.557199.80.038
6.78-5023.45801.661197.30.032

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
Coot3.22model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.283 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.79
RfactorNum. reflection% reflection
Rfree0.2571 506 5.12 %
Rwork0.2224 --
obs0.2243 9874 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.72 Å2 / Biso mean: 69.22 Å2 / Biso min: 36.22 Å2
Refinement stepCycle: final / Resolution: 2.5→32.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 6 0 1539
Biso mean--55.66 --
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011577
X-RAY DIFFRACTIONf_angle_d1.3682119
X-RAY DIFFRACTIONf_chiral_restr0.056209
X-RAY DIFFRACTIONf_plane_restr0.007270
X-RAY DIFFRACTIONf_dihedral_angle_d14.628594
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A867X-RAY DIFFRACTION10.866TORSIONAL
12C867X-RAY DIFFRACTION10.866TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4999-2.75130.35471130.296122852398100
2.7513-3.14920.41841230.318423162439100
3.1492-3.96650.31971260.2432311243799
3.9665-32.28520.18991440.18062456260099
Refinement TLS params.Method: refined / Origin x: -5.1384 Å / Origin y: 0.3988 Å / Origin z: -18.7748 Å
111213212223313233
T0.4755 Å2-0.0009 Å2-0.0684 Å2-0.4936 Å2-0.0288 Å2--0.4693 Å2
L0.6909 °2-0.4174 °20.3326 °2-0.6486 °20.3295 °2--0.5186 °2
S0.0376 Å °-0.1543 Å °0.056 Å °0.1166 Å °0.1141 Å °-0.0453 Å °0.3221 Å °-0.0048 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC310 - 400
2X-RAY DIFFRACTION1allA310 - 401
3X-RAY DIFFRACTION1all1

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