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- PDB-5eup: Structure of the Drosophila melanogaster CP190 BTB domain -

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Basic information

Entry
Database: PDB / ID: 5eup
TitleStructure of the Drosophila melanogaster CP190 BTB domain
ComponentsCentrosome-associated zinc finger protein CP190
KeywordsSTRUCTURAL PROTEIN / BTB domain CP190 chromatin insulator centrosome
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 / chromatin looping / polytene chromosome / 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 / chromatin looping / polytene chromosome / 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 / metal ion binding / nucleus / identical protein binding / 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 / SAD / Resolution: 2.5 Å
AuthorsPlevock, K.M. / Galletta, B.J. / Slep, K.C. / Rusan, N.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R01GM094415 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH T32GM008570 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1ZIAHL006104 United States
CitationJournal: Plos One / Year: 2015
Title: Newly Characterized Region of CP190 Associates with Microtubules and Mediates Proper Spindle Morphology in Drosophila Stem Cells.
Authors: Plevock, K.M. / Galletta, B.J. / Slep, K.C. / Rusan, N.M.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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
A: Centrosome-associated zinc finger protein CP190


Theoretical massNumber of molelcules
Total (without water)16,1771
Polymers16,1771
Non-polymers00
Water1448
1
A: Centrosome-associated zinc finger protein CP190

A: Centrosome-associated zinc finger protein CP190


Theoretical massNumber of molelcules
Total (without water)32,3532
Polymers32,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area3480 Å2
ΔGint-37 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.224, 86.224, 40.201
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: 16176.713 Da / Num. of mol.: 1 / Fragment: UNP residues 1-135
Source method: isolated from a genetically manipulated source
Details: N-terminal residues: GSH are a cloning artifact from placing the construct into pET28. Thrombin was used to remove the N-terminal His tag, leaving the N-terminal residues:GSH.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cp190, E(mod)4-1, CG6384 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(E3) pLysS / References: UniProt: Q24478
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Well condition = 1 ml of 20% PEG 3350 (w/v), 160 mM ammonium citrate dibasic. The initial hanging drop contained 2 micro liters of the mother liquor plus 2 micro liters of 15 mg/ml CP190 BTB domain.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98038 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98038 Å / Relative weight: 1
ReflectionResolution: 2.5→28.223 Å / Num. obs: 6124 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rsym value: 0.058 / Net I/σ(I): 23.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→28.223 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 606 10.17 %Random selection
Rwork0.219 ---
obs0.2233 5958 96.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→28.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 8 985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002994
X-RAY DIFFRACTIONf_angle_d0.551343
X-RAY DIFFRACTIONf_dihedral_angle_d12.417366
X-RAY DIFFRACTIONf_chiral_restr0.039157
X-RAY DIFFRACTIONf_plane_restr0.001169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.75120.36911390.31671228X-RAY DIFFRACTION91
2.7512-3.14890.29741500.26251350X-RAY DIFFRACTION98
3.1489-3.96550.2771550.23281366X-RAY DIFFRACTION99
3.9655-28.22520.22911620.19061408X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.28861.8811-1.5258.316-6.13024.4747-0.58241.3927-0.5545-1.02270.3121-0.9190.48680.56830.1920.6169-0.29340.0071.2322-0.31460.81618.7818-44.262816.2789
27.60974.6498-1.23348.28414.2665.83820.30920.34171.0261-0.1574-0.26571.0574-0.0463-1.2661-0.15420.5174-0.0451-0.07830.84760.11650.668523.3383-23.52392.6497
38.08011.9964-4.89465.40020.65325.0553-0.06990.394-0.2112-0.22670.1508-0.1766-0.02330.0306-0.18810.5997-0.0735-0.07770.64060.02750.454837.7164-31.99170.2327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 121 )

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