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- PDB-3b8a: Crystal structure of yeast hexokinase PI in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 3b8a
TitleCrystal structure of yeast hexokinase PI in complex with glucose
ComponentsHexokinase-1
KeywordsTRANSFERASE / induced fit / Allosteric enzyme / ATP-binding / Glycolysis / Kinase / Nucleotide-binding / Phosphorylation
Function / homology
Function and homology information


fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process ...fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / mannose metabolic process / glucose binding / fructose metabolic process / cellular glucose homeostasis / glucose import / Neutrophil degranulation / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase / Hexokinase domain signature. ...Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Hexokinase-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å
AuthorsKuser, P. / Cupri, F. / Bleicher, L. / Polikarpov, I.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of yeast hexokinase PI in complex with glucose: A classical "induced fit" example revised.
Authors: Kuser, P. / Cupri, F. / Bleicher, L. / Polikarpov, I.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Hexokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0803
Polymers53,8041
Non-polymers2762
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.120, 78.870, 144.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hexokinase-1 / / Hexokinase-A / Hexokinase PI


Mass: 53804.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04806, hexokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6.5
Details: 30% PEG 4000, 0.1M phosphate buffer, 10 mg/ml protein concentration, pH 6.5, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 1999
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.95→12.92 Å / Num. all: 14357 / Num. obs: 14357 / % possible obs: 92.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 47.358 Å2 / Rsym value: 0.119 / Net I/σ(I): 8.8
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1007 / Rsym value: 0.477 / % possible all: 94.44

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementStarting model: PDB ENTRY 1IG8
Resolution: 2.95→12.92 Å / FOM work R set: 0.828 / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ml
Details: Used group refinement for B-factors (one per residue)
RfactorNum. reflection% reflectionSelection details
Rfree0.244 715 4.98 %RANDOM
Rwork0.192 ---
all-15560 --
obs-14357 92.27 %-
Solvent computationBsol: 24.278 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 122.45 Å2 / Biso mean: 44.81 Å2 / Biso min: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.032 Å20 Å2-0 Å2
2--4.388 Å20 Å2
3----1.734 Å2
Refinement stepCycle: LAST / Resolution: 2.95→12.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 17 4 3684
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.471
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0391
X-RAY DIFFRACTIONf_dihedral_angle_d10.0761
X-RAY DIFFRACTIONf_plane_restr0.0011
X-RAY DIFFRACTIONf_nbd_refined4.0761

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