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- PDB-1dgk: MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH GLUCOS... -

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Entry
Database: PDB / ID: 1dgk
TitleMUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH GLUCOSE AND ADP IN THE ACTIVE SITE
ComponentsHEXOKINASE TYPE I
KeywordsTRANSFERASE / BRAIN HEXOKINASE / MAMMALIAN HEXOKINASE 1 / SUGAR KINASE
Function / homologyGlycolysis / Defective HK1 causes hexokinase deficiency (HK deficiency) / Hexokinase domain profile. / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase ...Glycolysis / Defective HK1 causes hexokinase deficiency (HK deficiency) / Hexokinase domain profile. / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase / hexokinase / hexokinase activity / establishment of protein localization to mitochondrion / maintenance of protein location in mitochondrion / carbohydrate phosphorylation / mannokinase activity / fructokinase activity / glucokinase activity / peptidoglycan binding / glucose binding / canonical glycolysis / positive regulation of interleukin-1 beta secretion / cellular glucose homeostasis / positive regulation of cytokine secretion involved in immune response / glycolytic process / mitochondrial outer membrane / membrane raft / mitochondrion / ATP binding / identical protein binding / cytosol / Hexokinase-1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.8 Å resolution
AuthorsAleshin, A.E. / Liu, X. / Kirby, C. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation.
Authors: Aleshin, A.E. / Kirby, C. / Liu, X. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Regulation of Hexokinase I: Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Phosphate
Authors: Aleshin, A.E. / Zeng, C. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#2: Journal: Structure / Year: 1998
Title: The Mechanism of Regulation of Hexokinase: New Insights from the Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Glucose-6-Phosphate
Authors: Aleshin, A.E. / Zeng, C. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 24, 1999 / Release: Mar 8, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 8, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 31, 2018Structure modelDatabase referencescitation_author_citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: HEXOKINASE TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8676
Polyers102,5571
Non-polymers1,3105
Water1,69394
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)145.780, 146.830, 58.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide HEXOKINASE TYPE I / HK I / BRAIN FORM HEXOKINASE


Mass: 102556.984 Da / Num. of mol.: 1
Details: SECOND MOLECULE OF ADP IS BOUND NEAR THE N-TERMINUS OF THE POLYPEPTIDE CHAIN. THE REGULATORY SITE ...SECOND MOLECULE OF ADP IS BOUND NEAR THE N-TERMINUS OF THE POLYPEPTIDE CHAIN. THE REGULATORY SITE OF THE N-TERMINAL DOMAIN IS OCCUPIED WITH GLUCOSE AND PHOSPHATE. MUTATIONS IN DIMER INTERFACE AND THE ACTIVE SITE
Mutation: E280A, R283A, G284Y, T536A / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cell: NEURON / Organ: BRAIN / Plasmid name: PET11A / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P19367, hexokinase
#2: Chemical ChemComp-GLC / ALPHA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 2 / Formula: C6H12O6 / Glucose
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Formula: H2O / Water

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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: 3.06 / Density percent sol: 59.76 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, SODIUM ACETATE, MES, ADP, GLUCOSE, GLUCOSE-6-PHOSPHATE. GROWN CRYSTALS WERE SOAKED WITH THE SAME BUFFER, BUT W/O GLUCOSE-6-PHOSPHATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and precipitant solutions
PH range low: 6.5 / PH range high: 5.8
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
120 mg/mlproteindrop
214-18 %(w/v)PEG8000reservoirprecipitant
3200 mMMESreservoirprecipitant
4200 mMsodium acetatereservoirprecipitant
520 mMADPreservoirprecipitant
62 mMreservoirprecipitantAl(NO3)3
710 mMreservoirprecipitantNaF
830 mMmagnesium acetatereservoirprecipitant

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Data collection

DiffractionMean temperature: 110 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 14-BM-D / Synchrotron site: APS / Beamline: 14-BM-D / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Feb 3, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 54 Å2 / D resolution high: 2.77 Å / D resolution low: 5 Å / Number all: 65575 / Number obs: 25465 / Rmerge I obs: 0.064 / NetI over sigmaI: 15 / Redundancy: 2.64 % / Percent possible obs: 78
Reflection shellRmerge I obs: 0.46 / Highest resolution: 2.77 Å / Lowest resolution: 2.98 Å / Redundancy: 2 % / Percent possible all: 57
Reflection
*PLUS
Number obs: 25491 / Number measured all: 65575 / Percent possible obs: 77.5
Reflection shell
*PLUS
Percent possible obs: 57 / Rmerge I obs: 0.44

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineDetails: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION.SIDE CHAINS OF RESIDUES 16, 17, 20, 21, 24, 101, 102, 252, 353, 794-799, 801, 804, 806, 809-811 HAVE POOR ELECTRON DENSITY. THEIR OCCUPANCIES ARE SET TO 0.01
R Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: ENGH & HUBER
Least-squares processR factor R free: 0.308 / R factor R work: 0.258 / R factor all: 0.26 / R factor obs: 0.26 / Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Number reflection R free: 1241 / Number reflection all: 23882 / Number reflection obs: 23882 / Percent reflection obs: 78
Refine hist #LASTHighest resolution: 2.8 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 7079 / Nucleic acid: 0 / Ligand: 83 / Solvent: 94 / Total: 7256
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.039
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.31 / R factor R work: 0.26
Refine LS restraints
*PLUS
Refine IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04

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