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- PDB-6er1: Crystal structure of BTB-domain of CP190 from D.melanogaster at h... -

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Basic information

Entry
Database: PDB / ID: 6er1
TitleCrystal structure of BTB-domain of CP190 from D.melanogaster at high resolution
ComponentsCentrosome-associated zinc finger protein CP190
KeywordsTRANSCRIPTION / Architectural protein / insulator / BTB-domain / CP190 / chromosome
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
PHOSPHATE ION / Centrosome-associated zinc finger protein Cp190
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Bonchuk, A.N. / Kachalova, G.S. / Georgiev, P.G. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and Science of the Russian Federation14.616.21.0066 Russian Federation
CitationJournal: Crystallography Reports / Year: 2017
Title: Purification, Isolation, Crystallization, and Preliminary X-ray Diffraction Study of the BTB Domain of the Centrosomal Protein 190 from Drosophila Melanogaster
Authors: Boyko, K.M. / Nikolaeva, A.Y. / Kachalova, G.S. / Bonchuk, A.N. / Popov, V.O.
History
DepositionOct 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3732
Polymers15,2781
Non-polymers951
Water2,252125
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)30,7454
Polymers30,5552
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area3640 Å2
ΔGint-47 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.940, 84.940, 40.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

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


Mass: 15277.722 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cp190, E(mod)4-1, CG6384 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24478
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: 0.1M HEPES pH 7.5; 0.8M Ammonium phosphate monobasic; 0.8 Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1,0
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
201
ReflectionResolution: 1.4→73.56 Å / Num. obs: 32673 / % possible obs: 98.2 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.4-1.424.20.58116390.8160.3180.664
7.67-73.564.30.072380.9790.0390.08

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data collection
Aimlessdata scaling
MOLREPmodel building
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U77

4u77


Resolution: 1.4→73.56 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.983 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0492 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 1539 4.7 %RANDOM
Rwork0.1459 ---
obs0.1476 31116 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.96 Å2 / Biso mean: 22.265 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å2-0 Å2
2---0.8 Å20 Å2
3---2.6 Å2
Refinement stepCycle: final / Resolution: 1.4→73.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 5 125 1118
Biso mean--24.5 36.99 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191040
X-RAY DIFFRACTIONr_bond_other_d0.0020.021024
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9671403
X-RAY DIFFRACTIONr_angle_other_deg2.34732357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3195120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95225.47253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54315205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.788154
X-RAY DIFFRACTIONr_chiral_restr0.1150.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
X-RAY DIFFRACTIONr_rigid_bond_restr2.60432064
X-RAY DIFFRACTIONr_sphericity_free38.515538
X-RAY DIFFRACTIONr_sphericity_bonded17.40352137
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 122 -
Rwork0.225 2308 -
all-2430 -
obs--99.75 %

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