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- PDB-1ig8: Crystal Structure of Yeast Hexokinase PII with the correct amino ... -

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Basic information

Entry
Database: PDB / ID: 1ig8
TitleCrystal Structure of Yeast Hexokinase PII with the correct amino acid sequence
Componentshexokinase PII
KeywordsTRANSFERASE / mixed alpha beta / two domains / cleft
Function / homology
Function and homology information


fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / regulation of transcription by glucose / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity ...fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / regulation of transcription by glucose / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / glucose binding / fructose metabolic process / regulation of cell size / glucose import / intracellular glucose homeostasis / negative regulation of apoptotic signaling pathway / Neutrophil degranulation / mitochondrial membrane / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. ...Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuser, P.R. / Krauchenco, S. / Antunes, O.A. / Polikarpov, I.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: The high resolution crystal structure of yeast hexokinase PII with the correct primary sequence provides new insights into its mechanism of action.
Authors: Kuser, P.R. / Krauchenco, S. / Antunes, O.A. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary Crystal Analysis of Yeast Hexokinase PI and PII
Authors: Kuser, P.R. / Golubev, A.M. / Polikarpov, I.
History
DepositionApr 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hexokinase PII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0972
Polymers54,0011
Non-polymers961
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.809, 142.809, 58.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein hexokinase PII / HEXOKINASE B


Mass: 54001.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04807, hexokinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.3-3.2M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6-2.4 Mammonium sulfate1reservoir
2100 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 1998
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.2→13 Å / Num. obs: 60395 / % possible obs: 95.1 % / Redundancy: 2.12 % / Biso Wilson estimate: 23.13 Å2 / Rsym value: 0.113
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.42 / Num. unique all: 1914 / % possible all: 96.6
Reflection
*PLUS
Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 96.6 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P152K mutant of yeast hexokinase

Resolution: 2.2→13 Å / SU B: 6.1415 / SU ML: 0.15315 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24781 / ESU R Free: 0.22644 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1368 5 %Random
Rwork0.162 ---
all-53732 --
obs-30146 --
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3671 0 5 441 4117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_planar_d0.0360.05

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