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- PDB-3geb: Crystal Structure of edeya2 -

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Basic information

Entry
Database: PDB / ID: 3geb
TitleCrystal Structure of edeya2
ComponentsEyes absent homolog 2
KeywordsHYDROLASE / Activator / Alternative splicing / Cytoplasm / Developmental protein / Magnesium / Nucleus / Polymorphism / Protein phosphatase / Transcription / Transcription regulation
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
Eyes absent homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, S.J.
CitationJournal: To be Published
Title: Structure of edeya2
Authors: Kim, S.J. / Jeong, D.G. / Jung, S.K. / Seong, E.R.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
B: Eyes absent homolog 2
C: Eyes absent homolog 2
D: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3158
Polymers124,2174
Non-polymers974
Water1,47782
1
A: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0792
Polymers31,0541
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0792
Polymers31,0541
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0792
Polymers31,0541
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0792
Polymers31,0541
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.612, 183.612, 120.150
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 /


Mass: 31054.330 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O00167, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 69.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2006 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11h,k,l10.65
11h,-k,-l20.35
ReflectionResolution: 2.4→50 Å / Num. all: 77791 / Num. obs: 76896 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11332 / Rsym value: 0.293 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal form is twinned by the operator h,-k,-l, twinning fraction 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3894 -random
Rwork0.171 ---
all0.175 76896 --
obs0.176 76896 98.7 %-
Displacement parametersBiso mean: 41.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8269 0 4 82 8355

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