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- PDB-7zrb: Crystal structure of Beta-catenin Armadillo repeats domain in com... -

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Basic information

Entry
Database: PDB / ID: 7zrb
TitleCrystal structure of Beta-catenin Armadillo repeats domain in complex with the inhibitor RS6452
ComponentsCatenin beta-1
KeywordsCELL ADHESION / beta-catenin / colon cancer / wnt pathway
Function / homology
Function and homology information


adherens junction / cell adhesion / cadherin binding / plasma membrane
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Chem-JKI / Catenin beta 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.434 Å
AuthorsCapelli, D. / Pochetti, G. / Montanari, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research Italy
CitationJournal: Acs Pharmacol Transl Sci / Year: 2023
Title: Novel N -(Heterocyclylphenyl)benzensulfonamide Sharing an Unreported Binding Site with T-Cell Factor 4 at the beta-Catenin Armadillo Repeats Domain as an Anticancer Agent.
Authors: Nalli, M. / Di Magno, L. / Wen, Y. / Liu, X. / D'Ambrosio, M. / Puxeddu, M. / Parisi, A. / Sebastiani, J. / Sorato, A. / Coluccia, A. / Ripa, S. / Di Pastena, F. / Capelli, D. / Montanari, R. ...Authors: Nalli, M. / Di Magno, L. / Wen, Y. / Liu, X. / D'Ambrosio, M. / Puxeddu, M. / Parisi, A. / Sebastiani, J. / Sorato, A. / Coluccia, A. / Ripa, S. / Di Pastena, F. / Capelli, D. / Montanari, R. / Masci, D. / Urbani, A. / Naro, C. / Sette, C. / Orlando, V. / D'Angelo, S. / Biagioni, S. / Bigogno, C. / Dondio, G. / Pastore, A. / Stornaiuolo, M. / Canettieri, G. / Liu, T. / Silvestri, R. / La Regina, G.
History
DepositionMay 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3463
Polymers117,9572
Non-polymers3891
Water1,54986
1
A: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3682
Polymers58,9781
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)58,9781
Polymers58,9781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.880, 160.240, 79.970
Angle α, β, γ (deg.)90.000, 99.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Catenin beta-1 /


Mass: 58978.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R8Y804
#2: Chemical ChemComp-JKI / 4-bromanyl-~{N}-(3-pyridin-2-ylphenyl)benzenesulfonamide


Mass: 389.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H13BrN2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 7-9% (w/v) PEG 6000, 100 mM Na Citrate, pH 5.6, 5 mM DTT, 15% (v/v) Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.43→78.84 Å / Num. obs: 12910 / % possible obs: 90.8 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.219 / Net I/σ(I): 7.3
Reflection shellResolution: 3.43→3.66 Å / Rmerge(I) obs: 1.882 / Mean I/σ(I) obs: 1 / Num. unique obs: 646 / CC1/2: 0.358

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SAINTdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TH1

1th1


Resolution: 3.434→45.264 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 787 6.1 %
Rwork0.2325 12116 -
obs0.2359 12903 77.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.2 Å2 / Biso mean: 79.9514 Å2 / Biso min: 33.52 Å2
Refinement stepCycle: final / Resolution: 3.434→45.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7673 0 23 86 7782
Biso mean--127.04 73.08 -
Num. residues----1007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037832
X-RAY DIFFRACTIONf_angle_d0.65310632
X-RAY DIFFRACTIONf_chiral_restr0.0381299
X-RAY DIFFRACTIONf_plane_restr0.0031360
X-RAY DIFFRACTIONf_dihedral_angle_d8.6864811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4341-3.64920.3583320.328652820
3.6492-3.93080.37291160.2877162964
3.9308-4.32610.31081300.2557220685
4.3261-4.95140.30991820.2333254899
4.9514-6.23570.3371520.26852621100
6.2357-45.2640.22281750.1927258499

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