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- PDB-4zs3: Structural complex of 5-aminofluorescein bound to the FTO protein -

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Basic information

Entry
Database: PDB / ID: 4zs3
TitleStructural complex of 5-aminofluorescein bound to the FTO protein
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsFLUORESCENT PROTEIN/INHIBITOR / FLUORESCENT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / : ...regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / DNA alkylation repair / oxidative demethylation / DNA demethylation / temperature homeostasis / mRNA destabilization / regulation of multicellular organism growth / adipose tissue development / ferrous iron binding / transferase activity / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FTO C-terminal domain / Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal / Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain / Alpha-ketoglutarate-dependent dioxygenase FTO / FTO, C-terminal domain superfamily / FTO catalytic domain / FTO C-terminal domain / FTO catalytic domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily ...FTO C-terminal domain / Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal / Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain / Alpha-ketoglutarate-dependent dioxygenase FTO / FTO, C-terminal domain superfamily / FTO catalytic domain / FTO C-terminal domain / FTO catalytic domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-A4F / 2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWang, T. / Hong, T. / Huang, Y. / Yang, C.G. / Zhou, X.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Fluorescein Derivatives as Bifunctional Molecules for the Simultaneous Inhibiting and Labeling of FTO Protein
Authors: Wang, T. / Hong, T. / Huang, Y. / Su, H. / Wu, F. / Chen, Y. / Wei, L. / Huang, W. / Hua, X. / Xia, Y. / Xu, J. / Gan, J. / Yuan, B. / Feng, Y. / Zhang, X. / Yang, C.G. / Zhou, X.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase FTO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4824
Polymers54,9341
Non-polymers5483
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-3 kcal/mol
Surface area20670 Å2
Unit cell
Length a, b, c (Å)142.239, 142.239, 83.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase FTO / Fat mass and obesity-associated protein


Mass: 54933.965 Da / Num. of mol.: 1 / Fragment: UNP residues 32-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C0B1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-A4F / 5-amino-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid / 5-aminofluorescein


Mass: 347.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13NO5
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHORS STATES THAT THE RING OF 5-AMINOFLUORESCEIN IS OPENED IN THE COMPLEX STRUCTURE 4ZS3.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.4 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, 11% PEG3350, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9735 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 23094 / % possible obs: 100 % / Redundancy: 10.4 % / Net I/σ(I): 27.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→28.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.715 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26257 1181 5.1 %RANDOM
Rwork0.20608 ---
obs0.20889 21848 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.274 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-1.54 Å20 Å2
2---1.54 Å2-0 Å2
3---5 Å2
Refinement stepCycle: 1 / Resolution: 2.45→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 37 52 3597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193640
X-RAY DIFFRACTIONr_bond_other_d0.0010.023384
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9594940
X-RAY DIFFRACTIONr_angle_other_deg0.7323.0017791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38724.317183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50515625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1951524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 83 -
Rwork0.32 1589 -
obs--98.99 %

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