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

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Basic information

Entry
Database: PDB / ID: 2hqq
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 binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion ...Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / 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 / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single Isomorphous Replacement / Resolution: 1.86 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 19, 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: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0564
Polymers32,7681
Non-polymers2883
Water4,828268
1
A: Ketohexokinase
hetero molecules

A: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1138
Polymers65,5372
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)61.260, 109.619, 146.290
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-531-

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

#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.75 Å3/Da / Density % sol: 67.17 %
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: PX14.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2003 / Details: mirrors
RadiationMonochromator: Si 111 optimized for 0.9795 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→87.706 Å / Num. all: 41681 / Num. obs: 41681 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 6.6
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5 / Num. unique all: 6030 / Rsym value: 0.325 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: Single Isomorphous Replacement
Starting model: PDB ENTRY 1RKD

1rkd


Resolution: 1.86→87.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.689 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23384 4129 10 %RANDOM
Rwork0.20474 ---
obs0.20768 37359 99.27 %-
all-41795 --
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: 26.285 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--1.38 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.86→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 15 268 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222332
X-RAY DIFFRACTIONr_bond_other_d0.0010.022141
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9533159
X-RAY DIFFRACTIONr_angle_other_deg0.70234963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59923.558104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29415390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_nbd_refined0.2170.3476
X-RAY DIFFRACTIONr_nbd_other0.2030.32154
X-RAY DIFFRACTIONr_nbtor_refined0.1880.51160
X-RAY DIFFRACTIONr_nbtor_other0.0880.51394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5352
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0650.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.76421895
X-RAY DIFFRACTIONr_mcbond_other0.2842608
X-RAY DIFFRACTIONr_mcangle_it2.0332355
X-RAY DIFFRACTIONr_scbond_it1.3492994
X-RAY DIFFRACTIONr_scangle_it2.0263804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 276 -
Rwork0.254 2746 -
obs--98.95 %

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