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- PDB-3hb1: Crystal structure of ed-eya2 complexed with Alf3 -

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Basic information

Entry
Database: PDB / ID: 3hb1
TitleCrystal structure of ed-eya2 complexed with Alf3
ComponentsEyes absent homolog 2 (Drosophila)
KeywordsHYDROLASE / alpha/beta hydrolase
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
ALUMINUM FLUORIDE / Eyes absent homolog 2 / Eyes absent homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsJung, S.K. / Jeong, D.G. / Ryu, S.E. / Kim, S.J.
CitationJournal: Faseb J. / Year: 2010
Title: Crystal structure of ED-Eya2: insight into dual roles as a protein tyrosine phosphatase and a transcription factor
Authors: Jung, S.K. / Jeong, D.G. / Chung, S.J. / Kim, J.H. / Park, B.C. / Tonks, N.K. / Ryu, S.E. / Kim, S.J.
History
DepositionMay 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eyes absent homolog 2 (Drosophila)
B: Eyes absent homolog 2 (Drosophila)
C: Eyes absent homolog 2 (Drosophila)
D: Eyes absent homolog 2 (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,70712
Polymers124,2734
Non-polymers4338
Water2,576143
1
A: Eyes absent homolog 2 (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1773
Polymers31,0681
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eyes absent homolog 2 (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1773
Polymers31,0681
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Eyes absent homolog 2 (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1773
Polymers31,0681
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Eyes absent homolog 2 (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1773
Polymers31,0681
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.941, 183.941, 119.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Eyes absent homolog 2 (Drosophila)


Mass: 31068.354 Da / Num. of mol.: 4 / Fragment: Eya domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q86U84, UniProt: O00167*PLUS, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4M NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→40 Å / Num. all: 69110 / Num. obs: 68962 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Rsym value: 0.071 / Net I/σ(I): 35.5
Reflection shellResolution: 2.51→2.59 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.268

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Processing

Software
NameClassification
HKL-3000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GEB

3geb


Resolution: 2.51→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3066 -random
Rwork0.2 ---
all0.205 69066 --
obs0.205 62438 90.4 %-
Refinement stepCycle: LAST / Resolution: 2.51→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8269 0 20 143 8432

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