[English] 日本語
Yorodumi
- PDB-2yhx: SEQUENCING A PROTEIN BY X-RAY CRYSTALLOGRAPHY. II. REFINEMENT OF ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / regulation of transcription by glucose / fructose import across plasma membrane / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / regulation of transcription by glucose / fructose import across plasma membrane / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / D-glucose binding / fructose metabolic process / regulation of cell size / D-glucose import / intracellular glucose homeostasis / negative regulation of apoptotic signaling pathway / Neutrophil degranulation / glycolytic process / mitochondrial membrane / 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 / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEXOKINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1492
Polymers45,8521
Non-polymers2971
Water00
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.

-
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
Data collection

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more