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- PDB-9cx8: Crystal structure of Human FN3K in apo-state -

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Basic information

Entry
Database: PDB / ID: 9cx8
TitleCrystal structure of Human FN3K in apo-state
ComponentsFructosamine-3-kinase
KeywordsTRANSFERASE / kinase / apo-state
Function / homology
Function and homology information


protein-fructosamine 3-kinase / fructosamine metabolic process / fructoselysine metabolic process / protein deglycation / protein-fructosamine 3-kinase activity / protein-ribulosamine 3-kinase / protein-ribulosamine 3-kinase activity / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / epithelial cell differentiation / post-translational protein modification ...protein-fructosamine 3-kinase / fructosamine metabolic process / fructoselysine metabolic process / protein deglycation / protein-fructosamine 3-kinase activity / protein-ribulosamine 3-kinase / protein-ribulosamine 3-kinase activity / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / epithelial cell differentiation / post-translational protein modification / kinase activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
Fructosamine/Ketosamine-3-kinase / Fructosamine kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Fructosamine-3-kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsGarg, A. / On, K.F. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2025
Title: The molecular basis of Human FN3K mediated phosphorylation of glycated substrates.
Authors: Garg, A. / On, K.F. / Xiao, Y. / Elkayam, E. / Cifani, P. / David, Y. / Joshua-Tor, L.
History
DepositionJul 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructosamine-3-kinase
B: Fructosamine-3-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,06729
Polymers66,0172
Non-polymers2,05027
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-129 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.351, 111.528, 132.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fructosamine-3-kinase / Protein-psicosamine 3-kinase FN3K / Protein-ribulosamine 3-kinase FN3K


Mass: 33008.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN3K / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H479, protein-fructosamine 3-kinase, protein-ribulosamine 3-kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M ammonium sulfate, 0.1 M tri-sodium citrate, and 1 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2020
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.67→132.6 Å / Num. obs: 90249 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.99 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.8
Reflection shellResolution: 1.67→1.7 Å / Rmerge(I) obs: 0.73 / Num. unique obs: 8938 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487-0000refinement
Cootmodel building
RAPDdata processing
PHASERphasing
RAPDdata reduction
RAPDdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→85.35 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 4457 4.94 %
Rwork0.1748 --
obs0.1763 90167 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→85.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 119 593 5317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174832
X-RAY DIFFRACTIONf_angle_d1.4556516
X-RAY DIFFRACTIONf_dihedral_angle_d13.677661
X-RAY DIFFRACTIONf_chiral_restr0.096668
X-RAY DIFFRACTIONf_plane_restr0.012844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.32291490.26762715X-RAY DIFFRACTION94
1.69-1.710.25341390.25152834X-RAY DIFFRACTION99
1.71-1.730.28461410.23882808X-RAY DIFFRACTION99
1.73-1.750.25981450.2412852X-RAY DIFFRACTION99
1.75-1.770.27721380.23232845X-RAY DIFFRACTION99
1.77-1.80.34981700.27672808X-RAY DIFFRACTION99
1.8-1.820.28661540.2662824X-RAY DIFFRACTION99
1.82-1.850.26621590.23822799X-RAY DIFFRACTION99
1.85-1.880.28241430.2312851X-RAY DIFFRACTION99
1.88-1.910.28931400.21472827X-RAY DIFFRACTION99
1.91-1.940.22121450.19342849X-RAY DIFFRACTION98
1.94-1.980.22311640.19212730X-RAY DIFFRACTION97
1.98-2.020.21721380.18232890X-RAY DIFFRACTION99
2.02-2.060.19461520.18192832X-RAY DIFFRACTION100
2.06-2.10.22581740.17712858X-RAY DIFFRACTION100
2.1-2.150.23371540.18912839X-RAY DIFFRACTION100
2.15-2.20.21841470.18962883X-RAY DIFFRACTION100
2.2-2.260.20291580.17232870X-RAY DIFFRACTION100
2.26-2.330.21941350.16912866X-RAY DIFFRACTION100
2.33-2.410.21351570.16632878X-RAY DIFFRACTION100
2.41-2.490.21081310.16662897X-RAY DIFFRACTION100
2.49-2.590.20221530.16882889X-RAY DIFFRACTION100
2.59-2.710.18341540.17682856X-RAY DIFFRACTION100
2.71-2.850.21761330.18032930X-RAY DIFFRACTION100
2.85-3.030.23431450.18242893X-RAY DIFFRACTION100
3.03-3.270.18981490.17922900X-RAY DIFFRACTION99
3.27-3.590.17831320.1572787X-RAY DIFFRACTION95
3.59-4.110.16281520.13682885X-RAY DIFFRACTION97
4.12-5.180.1671500.13522956X-RAY DIFFRACTION99
5.18-85.350.18511560.18183059X-RAY DIFFRACTION97

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