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- PDB-2yhx: SEQUENCING A PROTEIN BY X-RAY CRYSTALLOGRAPHY. II. REFINEMENT OF ... -

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Entry
Database: PDB / ID: 2yhx
TitleSEQUENCING A PROTEIN BY X-RAY CRYSTALLOGRAPHY. II. REFINEMENT OF YEAST HEXOKINASE B CO-ORDINATES AND SEQUENCE AT 2.1 ANGSTROMS RESOLUTION
ComponentsHEXOKINASE B
KeywordsTRANSFERASE(PHOSPHORYL / ALCOHOL ACCEPTOR)
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
Chem-OTG / Hexokinase-2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSteitz, T.A. / Anderson, C.M. / Stenkamp, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1978
Title: Sequencing a protein by x-ray crystallography. II. Refinement of yeast hexokinase B co-ordinates and sequence at 2.1 A resolution.
Authors: Anderson, C.M. / Stenkamp, R.E. / Steitz, T.A.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: Sequencing a Protein by X-Ray Crystallography. I. Interpretation of Yeast Hexokinase B at 2.5 Angstroms Resolution by Model Building
Authors: Anderson, C.M. / Mcdonald, R.C. / Steitz, T.A.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: A Refined Model of the Sugar Binding Site of Yeast Hexokinase B
Authors: Anderson, C.M. / Stenkamp, R.E. / Mcdonald, R.C. / Steitz, T.A.
#3: Journal: J.Biol.Chem. / Year: 1977
Title: High Resolution Crystal Structures of Yeast Hexokinase Complexes with Substrates, Activators, and Inhibitors. Evidence for an Allosteric Control Site
Authors: Steitz, T.A. / Anderson, W.F. / Fletterick, R.J. / Anderson, C.M.
#4: Journal: J.Mol.Biol. / Year: 1976
Title: High Resolution X-Ray Structure of Yeast Hexokinase, an Allosteric Protein Exhibiting a Non-Symmetric Arrangement of Subunits
Authors: Steitz, T.A. / Fletterick, R.J. / Anderson, W.F. / Anderson, C.M.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: The Structure of a Yeast Hexokinase Monomer and its Complexes with Substrates at 2.7-Angstroms Resolution
Authors: Fletterick, R.J. / Bates, D.J. / Steitz, T.A.
#6: Journal: J.Mol.Biol. / Year: 1975
Title: Structure of Yeast Hexokinase. Iv. Low-Resolution Structure of Enzyme-Substrate Complexes Revealing Negative Co-Operativity and Allosteric Interactions
Authors: Anderson, W.F. / Steitz, T.A.
#7: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of Yeast Hexokinase. III. Low Resolution Structure of a Second Crystal Form Showing a Different Quaternary Structure, Heterologous Interaction of Subunits and Substrate Binding
Authors: Anderson, W.F. / Fletterick, R.J. / Steitz, T.A.
#8: Journal: J.Mol.Biol. / Year: 1973
Title: Structure of Yeast Hexokinase. II. A 6 Angstroms Resolution Electron Density Map Showing Molecular Shape and Heterologous Interaction of Subunits
Authors: Steitz, T.A. / Fletterick, R.J. / Hwang, K.J.
#9: Journal: J.Mol.Biol. / Year: 1971
Title: Structure of Yeast Hexokinase-B. I. Preliminary X-Ray Studies and Subunit Structure
Authors: Steitz, T.A.
History
DepositionMar 20, 1978Processing site: BNL
SupersessionMay 23, 1978ID: 1YHX
Revision 1.0May 23, 1978Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEXOKINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1492
Polymers45,8521
Non-polymers2971
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.500, 59.200, 58.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE DENOTED *GAM* BY DEPOSITOR. / 2: RESIDUE DENOTED *DEL* BY DEPOSITOR. / 3: RESIDUE DENOTED *EPS* BY DEPOSITOR.

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Components

#1: Protein HEXOKINASE B


Mass: 45851.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P04807*PLUS, hexokinase
#2: Sugar ChemComp-OTG / 2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-alpha-D-glucopyranose / ORTHO-TOLUOYLGLUCOSAMINE / N-[(2-methylphenyl)carbonyl]-alpha-D-glucosamine / 2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-alpha-D-glucose / 2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-D-glucose / 2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-glucose


Type: D-saccharide, alpha linking / Mass: 297.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO6
Compound detailsTHIS CRYSTALLINE MODIFICATION CONTAINS ONE MONOMER PER ASYMMETRIC UNIT AND IS DESIGNATED B III. ...THIS CRYSTALLINE MODIFICATION CONTAINS ONE MONOMER PER ASYMMETRIC UNIT AND IS DESIGNATED B III. REFERENCE 4 (ABOVE) CONTAINS INFORMATION ON THE TRANSFORMATIONS WHICH RELATE THE COORDINATES OF THIS SET TO THOSE OF OTHER CRYSTALLINE FORMS.
Nonpolymer detailsTHE COORDINATES OF O-TOLUOYLGLUCOSAMINE (OTG), A COMPETITIVE INHIBITOR OF GLUCOSE BINDING, WERE ...THE COORDINATES OF O-TOLUOYLGLUCOSAMINE (OTG), A COMPETITIVE INHIBITOR OF GLUCOSE BINDING, WERE ALSO REFINED AND ARE INCLUDED HERE. THE GLUCOSE MOIETY OF OTG BINDS TO HEXOKINASE IN THE CRYSTAL IN AN IDENTICAL ORIENTATION AS GLUCOSE ITSELF.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal grow
*PLUS
pH: 7 / Method: microdialysis / Details: took from Anderson et al., from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %enzyme1buttom
22.1 Mpotassium phosphate1reservior
30.4 mMo-toluoylglucosamine1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.25

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 21 0 3311
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Rfactor obs: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONo_bond_d0.05
X-RAY DIFFRACTIONo_angle_d0.1

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