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- PDB-4u77: BTB domain from Drosophila CP190 -

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Basic information

Entry
Database: PDB / ID: 4u77
TitleBTB domain from Drosophila CP190
ComponentsCentrosome-associated zinc finger protein CP190
KeywordsTRANSCRIPTION / BTB fold / dimer / peptide binding groove
Function / homology
Function and homology information


nuclear axial expansion / Generic Transcription Pathway / heterochromatin boundary formation / chromatin insulator sequence binding / polytene chromosome band / POZ domain binding / polytene chromosome / chromatin looping / regulation of cytoskeleton organization / pericentriolar material ...nuclear axial expansion / Generic Transcription Pathway / heterochromatin boundary formation / chromatin insulator sequence binding / polytene chromosome band / POZ domain binding / polytene chromosome / chromatin looping / regulation of cytoskeleton organization / pericentriolar material / condensed chromosome / spindle microtubule / microtubule binding / DNA-binding transcription factor activity, RNA polymerase II-specific / centrosome / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Centrosome-associated zinc finger protein Cp190
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAllemand, F. / Cohen-Gonsaud, M. / Labesse, G. / Nollmann, M.
CitationJournal: Plos Genet. / Year: 2014
Title: Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome.
Authors: Vogelmann, J. / Le Gall, A. / Dejardin, S. / Allemand, F. / Gamot, A. / Labesse, G. / Cuvier, O. / Negre, N. / Cohen-Gonsaud, M. / Margeat, E. / Nollmann, M.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosome-associated zinc finger protein CP190
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7963
Polymers16,6261
Non-polymers1702
Water93752
1
A: Centrosome-associated zinc finger protein CP190
hetero molecules

A: Centrosome-associated zinc finger protein CP190
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5936
Polymers33,2522
Non-polymers3404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)84.979, 84.979, 40.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Centrosome-associated zinc finger protein CP190 / Protein enhancer of mod(mdg4)4-1 / dMAP190


Mass: 16626.199 Da / Num. of mol.: 1 / Fragment: UNP residues 1-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cp190, E(mod)4-1, CG6384 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q24478
#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
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.74 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: Na/K PO4 1.6 M, HEPES 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.03→42.49 Å / Num. all: 11252 / Num. obs: 11252 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 46.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 16.6
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.516 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→36.797 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1020 4.78 %
Rwork0.1913 --
obs0.1937 11252 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.6 Å2
Refinement stepCycle: LAST / Resolution: 2.03→36.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 10 52 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071014
X-RAY DIFFRACTIONf_angle_d1.0371369
X-RAY DIFFRACTIONf_dihedral_angle_d14.687370
X-RAY DIFFRACTIONf_chiral_restr0.04160
X-RAY DIFFRACTIONf_plane_restr0.005172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0302-2.13720.33771350.28472914X-RAY DIFFRACTION100
2.1372-2.27110.27141490.24742887X-RAY DIFFRACTION100
2.2711-2.44640.26131380.21462898X-RAY DIFFRACTION100
2.4464-2.69250.27681550.21962902X-RAY DIFFRACTION100
2.6925-3.0820.23731610.20322874X-RAY DIFFRACTION100
3.082-3.88230.23691580.18212903X-RAY DIFFRACTION100
3.8823-36.8030.22131240.16972929X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.79383.04563.58444.2914.07935.0886-0.30760.46120.0073-0.30270.412-0.2788-0.28090.9141-0.13540.3919-0.14060.01450.91330.10160.6058-18.689934.75259.2529
24.38532.4999-0.65313.2394-1.4375.3661-0.06170.2152-0.4811-0.16630.108-0.30980.45271.2496-0.04010.27690.05950.0190.6091-0.08690.5255-25.717822.39792.8346
33.0631-0.58873.34264.32340.05618.3234-0.08830.21220.3883-0.034-0.0435-0.0492-0.12840.30790.0660.2144-0.04860.02160.2915-0.00360.4098-37.288931.64990.0584
40.787-0.21070.58290.0839-0.02690.3212-0.17190.3254-0.1596-0.1357-0.0341-0.0921-0.01950.1165-0.04450.332-0.06290.03850.3830.0530.4788-31.275931.34142.6586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:52)
2X-RAY DIFFRACTION2chain 'A' and (resseq 53:90)
3X-RAY DIFFRACTION3chain 'A' and (resseq 91:121)
4X-RAY DIFFRACTION4chain 'S' and (resseq 20:232)

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