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- PDB-1glb: STRUCTURE OF THE REGULATORY COMPLEX OF ESCHERICHIA COLI IIIGLC WI... -

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Basic information

Entry
Database: PDB / ID: 1glb
TitleSTRUCTURE OF THE REGULATORY COMPLEX OF ESCHERICHIA COLI IIIGLC WITH GLYCEROL KINASE
Components
  • GLUCOSE-SPECIFIC PROTEIN IIIGlc
  • GLYCEROL KINASE
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / regulation of carbohydrate utilization / glycerol-3-phosphate metabolic process / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / glycerol kinase / glycerol kinase activity / glycerol metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system ...negative regulation of carbohydrate metabolic process / regulation of carbohydrate utilization / glycerol-3-phosphate metabolic process / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / glycerol kinase / glycerol kinase activity / glycerol metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / glycerol catabolic process / kinase activity / DNA damage response / zinc ion binding / ATP binding / metal ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
: / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / FGGY family of carbohydrate kinases signature 2. ...: / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / Duplicated hybrid motif / ATPase, nucleotide binding domain / Distorted Sandwich / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glycerol kinase / PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsHurley, J.H. / Worthylake, D. / Faber, H.R. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J.
CitationJournal: Science / Year: 1993
Title: Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase.
Authors: Hurley, J.H. / Faber, H.R. / Worthylake, D. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J.
History
DepositionOct 28, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8234
Polymers74,3042
Non-polymers5192
Water00
1
F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,29416
Polymers297,2178
Non-polymers2,0778
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation3_555-x,y,-z1
Unit cell
Length a, b, c (Å)123.700, 124.900, 134.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsGLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL CONTAINS TETRAMERS OF GLYCEROL-GLUCOSE-SPECIFIC FACTOR III COMPLEX KINASE WITH EXACT 222 POINT-GROUP SYMMETRY. THE TETRAMER IS LOCATED AT THE INTERSECTION OF THREE TWO-FOLD AXES IN THE CRYSTAL LATTICE. THE FOLLOWING TRANSFORMATIONS WILL PRODUCE A TETRAMER OF THE COMPLEX WHEN APPLIED TO THE COORDINATES IN THIS ENTRY: TRANSFORM 1 (-X, 1-Y, Z) -1.0 0.0 0.0 0.0 0.0 -1.0 0.0 124.90 0.0 0.0 1.0 0.0 TRANSFORM 2 (X, 1-Y, -Z) 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 124.90 0.0 0.0 -1.0 0.0 TRANSFORM 3 (-X, Y, -Z) -1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0

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Components

#1: Protein GLUCOSE-SPECIFIC PROTEIN IIIGlc


Mass: 18141.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein GLYCEROL KINASE


Mass: 56162.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A6F3, glycerol kinase
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.73 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.5-0.8 Msodium acetate1drop
3100 mMMES1drop
40.5-0.8 Msodium acetate1reservoir
5100 mMMES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 24169 / % possible obs: 76 % / Num. measured all: 81994 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / Num. possible: 58 / Rmerge(I) obs: 0.232

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.205 / Rfactor obs: 0.205 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4985 0 33 0 5018
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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