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- PDB-3b3l: Crystal structures of alternatively-spliced isoforms of human ket... -

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Basic information

Entry
Database: PDB / ID: 3b3l
TitleCrystal structures of alternatively-spliced isoforms of human ketohexokinase
ComponentsKetohexokinase
KeywordsTRANSFERASE / Fructose kinase / Carbohydrate metabolism / Disease mutation / Phosphorylation
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTrinh, C.H. / Asipu, A. / Bonthron, D.T. / Phillips, S.E.V.
CitationJournal: To be Published
Title: Crystal structures of alternatively-spliced isoforms of human ketohexokinase
Authors: Trinh, C.H. / Asipu, A. / Bonthron, D.T. / Phillips, S.E.V.
History
DepositionOct 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence is based on the isoform c in the database, KHK_HUMAN.

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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)130,2484
Polymers130,2484
Non-polymers00
Water32418
1
A: Ketohexokinase
B: Ketohexokinase


Theoretical massNumber of molelcules
Total (without water)65,1242
Polymers65,1242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-15 kcal/mol
Surface area24510 Å2
MethodPISA
2
C: Ketohexokinase
D: Ketohexokinase


Theoretical massNumber of molelcules
Total (without water)65,1242
Polymers65,1242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-16 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.555, 140.704, 179.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ketohexokinase / Hepatic fructokinase


Mass: 32561.982 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG 3000, 0.1M sodium acetate, pH 4.2, 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: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2004 / Details: mirrors
RadiationMonochromator: Si 111 optimised for 1.488 angstrom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.9→110.432 Å / Num. all: 49962 / Num. obs: 49962 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 6.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7208 / Rsym value: 0.354 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HQQ

2hqq


Resolution: 2.9→25.38 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.88 / SU B: 31.049 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.577 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28074 2608 5.1 %RANDOM
Rwork0.23622 ---
all0.23843 48714 --
obs0.23843 48714 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.154 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--0.3 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.9→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8898 0 0 18 8916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229067
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.95312293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.39751180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2323.985399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.473151456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1111566
X-RAY DIFFRACTIONr_chiral_restr0.0930.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026950
X-RAY DIFFRACTIONr_nbd_refined0.2260.23871
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.25
X-RAY DIFFRACTIONr_mcbond_it3.75665996
X-RAY DIFFRACTIONr_mcangle_it5.65699354
X-RAY DIFFRACTIONr_scbond_it4.08163424
X-RAY DIFFRACTIONr_scangle_it5.96592939
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 203 -
Rwork0.359 3546 -
obs-3546 99.87 %
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)
12.1211-1.0778-0.71882.51650.52271.79680.08460.1392-0.2142-0.0306-0.26110.3414-0.0845-0.21730.1765-0.11560.03210.0115-0.1134-0.0691-0.104538.896833.56473.8643
22.3388-0.0983-0.11892.43770.12193.257-0.07360.7411-0.2169-0.7021-0.15490.2141-0.4332-0.41450.22860.13750.2247-0.20970.3275-0.3411-0.077650.626423.0701-37.5798
31.50060.22340.35832.26321.46464.0759-0.17990.4301-0.6257-0.2419-0.26520.2216-0.1787-0.56810.4452-0.0310.05950.02470.1081-0.44690.141822.857479.345759.4277
41.61140.021-0.29551.8510.8025.28560.2402-0.21890.9464-0.07810.01420.16-0.9742-0.407-0.25430.11610.03030.1210.0143-0.25870.482917.718774.53816.2375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2983 - 298
2X-RAY DIFFRACTION2BB3 - 2983 - 298
3X-RAY DIFFRACTION3CC3 - 2983 - 298
4X-RAY DIFFRACTION4DD3 - 2983 - 298

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