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- PDB-8omg: Crystal structure of mKHK (apo) -

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Basic information

Entry
Database: PDB / ID: 8omg
TitleCrystal structure of mKHK (apo)
ComponentsKetohexokinase
KeywordsSUGAR BINDING PROTEIN / Mouse KHK / Sugar Kinase / species difference / apo
Function / homology
Function and homology information


glycolytic process through fructose-1-phosphate / Fructose catabolism / fructose catabolic process / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / ketohexokinase / ketohexokinase activity / regulation of glycogen metabolic process / fructose metabolic process / ATP binding / nucleus ...glycolytic process through fructose-1-phosphate / Fructose catabolism / fructose catabolic process / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / ketohexokinase / ketohexokinase activity / regulation of glycogen metabolic process / fructose metabolic process / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ketohexokinase / : / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsEbenhoch, E. / Pautsch, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design.
Authors: Ebenhoch, R. / Bauer, M. / Romig, H. / Gottschling, D. / Kley, J.T. / Heine, N. / Weber, A. / Uphues, I. / Nar, H. / Pautsch, A.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase


Theoretical massNumber of molelcules
Total (without water)65,5572
Polymers65,5572
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-19 kcal/mol
Surface area25200 Å2
Unit cell
Length a, b, c (Å)154.390, 154.390, 50.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Ketohexokinase / Hepatic fructokinase


Mass: 32778.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Khk / Production host: Escherichia coli (E. coli) / References: UniProt: P97328, ketohexokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 14% PEG 8000, 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate pH 4.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.82→66.85 Å / Num. obs: 40725 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 33.94 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 15.3
Reflection shellResolution: 2.087→2.094 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 39776 / Rsym value: 0.981 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→66.85 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1964 4.94 %RANDOM
Rwork0.225 ---
obs0.226 39776 64.9 %-
Displacement parametersBiso max: 150.85 Å2 / Biso mean: 52.97 Å2 / Biso min: 15.49 Å2
Baniso -1Baniso -2Baniso -3
1--9.7755 Å20 Å20 Å2
2---9.7755 Å20 Å2
3---19.5509 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 1.82→66.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 0 231 4670
Biso mean---37.05 -
Num. residues----576
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1599SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes785HARMONIC5
X-RAY DIFFRACTIONt_it4522HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion572SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5045SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4522HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6109HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion16.96
LS refinement shellResolution: 1.82→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2652 39 4.9 %
Rwork0.2489 757 -
all0.2497 796 -
obs--12.33 %
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)
11.63220.99990.72723.09880.86142.42520.482-0.1482-0.1860.7491-0.0785-0.64850.7224-0.0827-0.4036-0.0732-0.0951-0.3824-0.46890.05450.1483-17.0279-63.628421.2469
21.3069-0.69580.31162.3895-0.43570.73930.13010.040.008-0.1349-0.01170.17320.0838-0.0593-0.1184-0.2294-0.0125-0.1048-0.22790.07930.3647-32.2167-28.4947-2.436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 297
2X-RAY DIFFRACTION2{ B|* }B4 - 297

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