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- PDB-2hlz: Crystal Structure of human ketohexokinase -

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Basic information

Entry
Database: PDB / ID: 2hlz
TitleCrystal Structure of human ketohexokinase
ComponentsKetohexokinaseHepatic fructokinase
KeywordsTRANSFERASE / non-protein kinase / creatine kinase / fructokinase / isoform A / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 1.85 Å
AuthorsRabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of human ketohexokinase (CASP Target)
Authors: Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Structure summary / Category: software / struct
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct.title
Remark 300Author states that biological unit for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
C: Ketohexokinase
D: Ketohexokinase


Theoretical massNumber of molelcules
Total (without water)137,22636
Polymers137,2264
Non-polymers032
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-26 kcal/mol
Surface area45370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.933, 71.672, 82.694
Angle α, β, γ (deg.)105.06, 107.33, 93.09
Int Tables number1
Space group name H-MP1
Detailsnot known

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Components

#1: Protein
Ketohexokinase / Hepatic fructokinase / Hepatic fructokinase


Mass: 34306.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) codon + RIL / References: UniProt: P50053, ketohexokinase
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.855.8
22.855.8
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 17% PEG8000, 5mM Cobalt Chloride, 200mM ammonium sulfate, 100mM NaCitrate, pH 4.2, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 113793 / % possible obs: 95.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Χ2: 1.214 / Net I/σ(I): 10
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.85-1.92773.20.43891850.871
1.92-1.9991.63.60.362109430.945
1.99-2.0896.53.80.268115530.987
2.08-2.1997.13.90.209115880.96
2.19-2.3397.43.90.172116391.093
2.33-2.5197.83.90.127117041.033
2.51-2.7698.13.90.094117321.112
2.76-3.1698.43.90.063117771.276
3.16-3.9898.83.90.038117901.422
3.98-3099.43.90.036118822.243

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Phasing

PhasingMethod: sad
Phasing MADD res high: 3.2 Å / D res low: 20 Å / FOM : 0.38 / Reflection: 22796
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se31.44700.00100.896
2Se28.5330.0340.0590.0670.823
3Se3.0150.9180.7730.7610.676
4Se15.0720.3880.3040.0060.736
5Se13.6060.6210.3460.7220.662
6Se9.4440.4090.3510.9570.711
7Se11.8940.0820.8440.9620.643
8Se17.4470.4280.4370.7950.611
9Se21.2520.0920.6880.790.63
10Se5.1420.8440.7340.6910.645
11Se26.1350.5760.3430.7770.702
12Se16.1330.3190.5110.9490.493
Phasing MAD shell
Resolution (Å)FOM Reflection
10.43-200.431222
6.96-10.430.471929
5.55-6.960.472413
4.75-5.550.432809
4.22-4.750.413204
3.83-4.220.293485
3.54-3.830.33741
3.3-3.540.353993
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0 / Reflection: 37519 / Reflection acentric: 37519 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
7.7-19.9860.880.8814481448
4.8-7.70.840.8449424942
3.9-4.80.860.8663316331
3.4-3.90.810.8163776377
2.9-3.40.630.631137511375
2.7-2.90.40.470467046

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
MolProbitymodel building
RefinementMethod to determine structure: SAS / Resolution: 1.85→29.656 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.203 / SU B: 3.027 / SU ML: 0.094 / ESU R: 0.149 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4258 3.762 %thin shells
Rwork0.2143 ---
all0.216 ---
obs-113173 94.572 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.733 Å21.125 Å2-0.201 Å2
2--0.371 Å2-0.035 Å2
3----1.121 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9045 0 32 372 9449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229225
X-RAY DIFFRACTIONr_bond_other_d0.0010.026200
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.96112527
X-RAY DIFFRACTIONr_angle_other_deg0.95315116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06951205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51223.721387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.883151497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7031564
X-RAY DIFFRACTIONr_chiral_restr0.0820.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021888
X-RAY DIFFRACTIONr_nbd_refined0.2030.21650
X-RAY DIFFRACTIONr_nbd_other0.1980.26032
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24357
X-RAY DIFFRACTIONr_nbtor_other0.0830.24715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2401
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.29
X-RAY DIFFRACTIONr_mcbond_it2.57826560
X-RAY DIFFRACTIONr_mcbond_other0.78822453
X-RAY DIFFRACTIONr_mcangle_it3.13539547
X-RAY DIFFRACTIONr_scbond_it2.74523580
X-RAY DIFFRACTIONr_scangle_it3.60432973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.85-1.8980.505110.31263400.312881372.064
1.898-1.9500.27374820.273862786.728
1.95-2.0060.2728800.23370030.237835494.362
2.006-2.06700.21878250.218811296.462
2.067-2.13500.20676130.206785696.907
2.135-2.2090.2627670.20766040.213762296.707
2.209-2.29200.27767540.277736491.716
2.292-2.3850.2635510.20363910.208712897.391
2.385-2.4910.2431030.265030.201676597.65
2.491-2.61100.20863310.208646697.912
2.611-2.7510.2575550.21155250.215619898.096
2.751-2.91700.22257330.222582698.404
2.917-3.1160.264180.22549940.228550098.4
3.116-3.3620.2752830.21947790.223513198.655
3.362-3.6790.265450.20345900.204469498.743
3.679-4.1050.2072360.18339920.185427998.808
4.105-4.7250.1961920.16435520.166377599.179
4.725-5.7510.2551060.19130600.193318899.31
5.751-7.9840.224710.24924220.248250399.6
7.984-29.6560.217400.21114220.211146799.659

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