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- PDB-5zma: Structural basis for an allosteric Eya2 phosphatase inhibitor -

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Basic information

Entry
Database: PDB / ID: 5zma
TitleStructural basis for an allosteric Eya2 phosphatase inhibitor
ComponentsEyes absent homolog 2
KeywordsTRANSCRIPTION / eya2 / eyes absent protein / phosphatase / transcription coactivator
Function / homology
Function and homology information


histone H2AXY142 phosphatase activity / mesodermal cell fate specification / striated muscle tissue development / mitochondrial outer membrane permeabilization / anatomical structure development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...histone H2AXY142 phosphatase activity / mesodermal cell fate specification / striated muscle tissue development / mitochondrial outer membrane permeabilization / anatomical structure development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell differentiation / DNA repair / magnesium ion binding / mitochondrion / nucleoplasm / nucleus / cytosol
Similarity search - Function
Rossmann fold - #12350 / EYA domain / Eyes absent family / EYA domain superfamily / EYA domain, metazoan / haloacid dehalogenase-like hydrolase / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9FX / Eyes absent homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.175 Å
AuthorsAnantharajan, J. / Jansson, A.E. / Kang, C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: Mol.Cancer Ther. / Year: 2019
Title: Structural and Functional Analyses of an Allosteric EYA2 Phosphatase Inhibitor That Has On-Target Effects in Human Lung Cancer Cells.
Authors: Anantharajan, J. / Zhou, H. / Zhang, L. / Hotz, T. / Vincent, M.Y. / Blevins, M.A. / Jansson, A.E. / Kuan, J.W.L. / Ng, E.Y. / Yeo, Y.K. / Baburajendran, N. / Lin, G. / Hung, A.W. / Joy, J. ...Authors: Anantharajan, J. / Zhou, H. / Zhang, L. / Hotz, T. / Vincent, M.Y. / Blevins, M.A. / Jansson, A.E. / Kuan, J.W.L. / Ng, E.Y. / Yeo, Y.K. / Baburajendran, N. / Lin, G. / Hung, A.W. / Joy, J. / Patnaik, S. / Marugan, J. / Rudra, P. / Ghosh, D. / Hill, J. / Keller, T.H. / Zhao, R. / Ford, H.L. / Kang, C.
History
DepositionApr 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: Eyes absent homolog 2
A: Eyes absent homolog 2
C: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1066
Polymers99,0793
Non-polymers1,0273
Water0
1
B: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3692
Polymers33,0261
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3692
Polymers33,0261
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3692
Polymers33,0261
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.985, 49.497, 144.957
Angle α, β, γ (deg.)90.000, 101.210, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Eyes absent homolog 2 /


Mass: 33026.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EYA2, EAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00167, protein-tyrosine-phosphatase
#2: Chemical ChemComp-9FX / 3-fluoro-N'-[(E)-{5-[(pyrimidin-2-yl)sulfanyl]furan-2-yl}methylidene]benzohydrazide


Mass: 342.348 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H11FN4O2S

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Hepes 7.5, 200mM Nacl, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9538 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 3.17→47.83 Å / Num. obs: 17212 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 85.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.054 / Rrim(I) all: 0.11 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.17-3.3940.64930160.8290.3640.74696.9
8.98-47.833.70.0258090.9990.0140.02897.7

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EGC

4egc


Resolution: 3.175→47.826 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.96
RfactorNum. reflection% reflection
Rfree0.2655 1727 10.04 %
Rwork0.2287 --
obs0.2324 17202 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.41 Å2 / Biso mean: 85.4502 Å2 / Biso min: 31.62 Å2
Refinement stepCycle: final / Resolution: 3.175→47.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 72 0 5963
Biso mean--61.02 --
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026098
X-RAY DIFFRACTIONf_angle_d0.5518279
X-RAY DIFFRACTIONf_chiral_restr0.039945
X-RAY DIFFRACTIONf_plane_restr0.0031050
X-RAY DIFFRACTIONf_dihedral_angle_d4.534067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.175-3.26840.36991360.3041241137795
3.2684-3.37390.37581420.294612551397100
3.3739-3.49440.30721410.27091291143299
3.4944-3.63430.29091430.26721265140899
3.6343-3.79960.29751440.25521311145599
3.7996-3.99990.29291400.2331246138699
3.9999-4.25030.30331460.225512941440100
4.2503-4.57830.25591440.20751292143699
4.5783-5.03850.23641440.211412951439100
5.0385-5.76650.2931480.240513061454100
5.7665-7.26120.26851500.25341324147499
7.2612-47.83130.18541490.18281355150499

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