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- PDB-1f3g: THREE-DIMENSIONAL STRUCTURE OF THE ESCHERICHIA COLI PHOSPHOCARRIE... -

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Basic information

Entry
Database: PDB / ID: 1f3g
TitleTHREE-DIMENSIONAL STRUCTURE OF THE ESCHERICHIA COLI PHOSPHOCARRIER PROTEIN III GLC
ComponentsGLUCOSE-SPECIFIC PHOSPHOCARRIER PROTEIN IIAGLC
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / regulation of carbohydrate utilization / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / membrane / metal ion binding / 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. / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWorthylake, D. / Meadow, N. / Roseman, S. / Liao, D.-I. / Herzberg, O. / Remington, S.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Three-dimensional structure of the Escherichia coli phosphocarrier protein IIIglc.
Authors: Worthylake, D. / Meadow, N.D. / Roseman, S. / Liao, D.I. / Herzberg, O. / Remington, S.J.
#1: Journal: J.Biol.Chem. / Year: 1987
Title: Sugar Transport by the Bacterial Phosphotransferase System. Molecular Cloning and Structural Analysis of the Escherichia Coli Ptsh, Ptsi and Crr Genes
Authors: Saffen, D.W. / Presper, K.A. / Doering, T.L. / Roseman, S.
History
DepositionAug 28, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSE-SPECIFIC PHOSPHOCARRIER PROTEIN IIAGLC


Theoretical massNumber of molelcules
Total (without water)17,3381
Polymers17,3381
Non-polymers00
Water39622
1
A: GLUCOSE-SPECIFIC PHOSPHOCARRIER PROTEIN IIAGLC

A: GLUCOSE-SPECIFIC PHOSPHOCARRIER PROTEIN IIAGLC

A: GLUCOSE-SPECIFIC PHOSPHOCARRIER PROTEIN IIAGLC


Theoretical massNumber of molelcules
Total (without water)52,0143
Polymers52,0143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)80.300, 80.300, 86.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein GLUCOSE-SPECIFIC PHOSPHOCARRIER PROTEIN IIAGLC


Mass: 17337.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P69783
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PT3G_ECOLI SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 169 NONE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
225 mMTris-HCl1drop
320 %(w/w)PEG80001dropprecipitant
4400 mMsodium acetate1dropprecipitant
5100 mMcacodylate1dropprecipitant
6precipitant1reservoir1ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 8279 / Num. measured all: 15038 / Rmerge(I) obs: 0.021

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.162 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 0 22 1137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 6 Å / Num. reflection obs: 7731 / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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