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- PDB-2hw1: Crystal structure of human ketohexokinase complexed to different ... -

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Basic information

Entry
Database: PDB / ID: 2hw1
TitleCrystal structure of human ketohexokinase complexed to different sugar molecules
ComponentsKetohexokinase
KeywordsTRANSFERASE / Fructose kinase
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ketohexokinase / : / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / beta-D-fructofuranose / Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsTrinh, C.H. / Asipu, A. / Bonthron, D.T. / Phillips, S.E.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structures of alternatively spliced isoforms of human ketohexokinase.
Authors: Trinh, C.H. / Asipu, A. / Bonthron, D.T. / Phillips, S.E.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6435
Polymers32,7681
Non-polymers8754
Water4,450247
1
A: Ketohexokinase
hetero molecules

A: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,28610
Polymers65,5372
Non-polymers1,7498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)61.264, 107.823, 146.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-845-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: 1-x,-y,z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Ketohexokinase / Hepatic fructokinase


Mass: 32768.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P50053, ketohexokinase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 250 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.7M ammonium sulphate, 0.5M lithium sulphate, 0.1M sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2003 / Details: mirrors
RadiationMonochromator: Si 111 optimized for 0.977 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.1→87.71 Å / Num. all: 27885 / Num. obs: 27885 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3744 / Rsym value: 0.34 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2HQQ

2hqq


Resolution: 2.1→87.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.939 / SU ML: 0.106 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22777 1416 5.1 %RANDOM
Rwork0.19263 ---
obs0.19441 26466 96.78 %-
all-27885 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--1.35 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 54 247 2578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222374
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9883222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72823.558104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96715390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6521519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021776
X-RAY DIFFRACTIONr_nbd_refined0.2240.31097
X-RAY DIFFRACTIONr_nbtor_refined0.3190.51607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.5373
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.522
X-RAY DIFFRACTIONr_mcbond_it1.25821505
X-RAY DIFFRACTIONr_mcangle_it2.09232355
X-RAY DIFFRACTIONr_scbond_it1.3262977
X-RAY DIFFRACTIONr_scangle_it2.1323867
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 89 -
Rwork0.252 1702 -
obs-1702 85.57 %

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