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- PDB-3muj: Early B-cell factor 3 (EBF3) IPT/TIG and dimerization helices -

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Basic information

Entry
Database: PDB / ID: 3muj
TitleEarly B-cell factor 3 (EBF3) IPT/TIG and dimerization helices
ComponentsTranscription factor COE3
KeywordsDNA BINDING PROTEIN / Immunoglobulin like fold / Helix-loop-heliX / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleus / metal ion binding
Similarity search - Function
Transcription factor COE / Transcription factor COE, conserved site / Transcription factor COE, DNA-binding domain / Transcription factor COE, helix-loop-helix domain / Transcription factor COE, IPT domain / Transcription factor COE, DNA-binding domain superfamily / Transcription factor COE1 DNA-binding domain / Transcription factor COE1 helix-loop-helix domain / COE family signature. / IPT/TIG domain ...Transcription factor COE / Transcription factor COE, conserved site / Transcription factor COE, DNA-binding domain / Transcription factor COE, helix-loop-helix domain / Transcription factor COE, IPT domain / Transcription factor COE, DNA-binding domain superfamily / Transcription factor COE1 DNA-binding domain / Transcription factor COE1 helix-loop-helix domain / COE family signature. / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription factor COE3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSiponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schueler, H. / Schutz, P. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Berglund, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif.
Authors: Siponen, M.I. / Wisniewska, M. / Lehtio, L. / Johansson, I. / Svensson, L. / Raszewski, G. / Nilsson, L. / Sigvardsson, M. / Berglund, H.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor COE3
B: Transcription factor COE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7507
Polymers30,4932
Non-polymers2575
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-38 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.680, 134.680, 41.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcription factor COE3 / Early B-cell factor 3


Mass: 15246.656 Da / Num. of mol.: 2 / Fragment: IPT/TIG and HLH domain (UNP residues 261-395)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ebf3, COE3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE / References: UniProt: Q9H4W6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 277 K / pH: 6.9
Details: 0.1M BTP, 0.2M Naformate, 21% PEG3350, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 26, 2009
Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.92→44.1 Å / Num. obs: 32303 / % possible obs: 94 % / Redundancy: 9.1 % / Biso Wilson estimate: 31.99 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 30.82
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.64 / Rsym value: 0.473 / % possible all: 17.3

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MQI

3mqi


Resolution: 1.92→44.1 Å / SU ML: 0.22 / σ(F): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.193 2004 6.2 %
Rwork0.17 --
obs0.171 32297 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.21 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9334 Å2-0 Å20 Å2
2---1.9334 Å2-0 Å2
3---3.8667 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.92→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 14 340 2415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152200
X-RAY DIFFRACTIONf_angle_d1.4763010
X-RAY DIFFRACTIONf_dihedral_angle_d17.086831
X-RAY DIFFRACTIONf_chiral_restr0.106344
X-RAY DIFFRACTIONf_plane_restr0.008386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.96290.25931110.20571702X-RAY DIFFRACTION76
1.9629-2.01590.21891350.18282035X-RAY DIFFRACTION93
2.0159-2.07520.22171420.17612171X-RAY DIFFRACTION98
2.0752-2.14220.21811480.16722186X-RAY DIFFRACTION100
2.1422-2.21880.19041380.16822167X-RAY DIFFRACTION98
2.2188-2.30760.22971470.1752203X-RAY DIFFRACTION99
2.3076-2.41260.20991470.1782195X-RAY DIFFRACTION99
2.4126-2.53980.21531490.18072204X-RAY DIFFRACTION100
2.5398-2.69890.18871440.17172194X-RAY DIFFRACTION99
2.6989-2.90720.2041480.16842211X-RAY DIFFRACTION99
2.9072-3.19960.19211500.18172226X-RAY DIFFRACTION99
3.1996-3.66230.20221520.16552221X-RAY DIFFRACTION100
3.6623-4.6130.14221420.1422257X-RAY DIFFRACTION100
4.613-38.88680.1781510.15712321X-RAY DIFFRACTION100

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