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- PDB-5dab: Crystal structure of FTO-IN115 -

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Basic information

Entry
Database: PDB / ID: 5dab
TitleCrystal structure of FTO-IN115
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsOXIDOREDUCTASE / Fat mass and obesity associated (FTO) protein / small molecule
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 / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity ...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 / snRNA processing / 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 / RNA repair / DNA alkylation repair / 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-58W / 2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsChai, J. / Zhou, B. / Liu, W. / Han, Z. / Niu, T.
CitationJournal: To Be Published
Title: Crystal structure of FTO-IN115
Authors: Chai, J. / Zhou, B. / Liu, W. / Han, Z. / Niu, T.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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.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_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,92913
Polymers55,0901
Non-polymers83912
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.681, 142.681, 81.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 55090.184 Da / Num. of mol.: 1 / Fragment: UNP residues 33-505
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

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Non-polymers , 5 types, 130 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: Cl
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-58W / N-(5-chloro-2,4-dihydroxyphenyl)-1-phenylcyclobutanecarboxamide


Mass: 317.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16ClNO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10%(w/v) polyethylene glycol (PEG) 3350, 0.1 M trisodium citrate dehydrate, 3.0 mM N-oxalylglycine (NOG)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 35070 / % possible obs: 96.7 % / Redundancy: 3.7 % / Net I/σ(I): 30.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdata reduction
PHENIXphasing
PHENIXdev_596refinement
RefinementResolution: 2.1→28.908 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1745 4.98 %
Rwork0.21 --
obs0.2116 35064 96.59 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.16 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.7916 Å20 Å20 Å2
2---7.7916 Å2-0 Å2
3---15.5831 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 42 118 3674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043631
X-RAY DIFFRACTIONf_angle_d0.8064927
X-RAY DIFFRACTIONf_dihedral_angle_d14.731359
X-RAY DIFFRACTIONf_chiral_restr0.059530
X-RAY DIFFRACTIONf_plane_restr0.003638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1004-2.16220.34311480.29972861X-RAY DIFFRACTION99
2.1622-2.2320.27661440.26612853X-RAY DIFFRACTION100
2.232-2.31170.31871480.24552896X-RAY DIFFRACTION100
2.3117-2.40420.29651510.25272864X-RAY DIFFRACTION100
2.4042-2.51360.28571490.23472842X-RAY DIFFRACTION100
2.5136-2.6460.27921420.2282932X-RAY DIFFRACTION100
2.646-2.81170.22431610.21262857X-RAY DIFFRACTION100
2.8117-3.02860.24441440.20892858X-RAY DIFFRACTION100
3.0286-3.3330.24721490.21582880X-RAY DIFFRACTION100
3.333-3.81430.21311460.19652768X-RAY DIFFRACTION97
3.8143-4.80210.2071410.17922504X-RAY DIFFRACTION88
4.8021-28.91070.25831220.21842204X-RAY DIFFRACTION77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6769-0.9818-0.94392.24150.19752.72920.0187-0.59360.2470.1440.15140.1305-0.1430.2921-0.09860.3168-0.00070.05580.3604-0.02310.3172-10.314230.42997.7876
24.3118-2.0217-1.52051.71121.48981.56650.56250.35350.1317-0.4885-0.4184-0.328-0.38850.1073-0.08110.58770.1960.09570.61870.04560.454414.525816.6872-14.1559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 27:327
2X-RAY DIFFRACTION2chain A and resi 328:500

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