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- PDB-2f3g: IIAGLC CRYSTAL FORM III -

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Basic information

Entry
Database: PDB / ID: 2f3g
TitleIIAGLC CRYSTAL FORM III
ComponentsGLUCOSE-SPECIFIC PHOSPHOCARRIER
KeywordsPHOSPHOTRANSFERASE / SIGNAL TRANSDUCTION / PHOSPHOCARRIER
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 / metal ion 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. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsFeese, M. / Comolli, L. / Meadow, N. / Roseman, S. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1997
Title: Structural studies of the Escherichia coli signal transducing protein IIAGlc: implications for target recognition.
Authors: Feese, M.D. / Comolli, L. / Meadow, N.D. / Roseman, S. / Remington, S.J.
History
DepositionOct 14, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSE-SPECIFIC PHOSPHOCARRIER
B: GLUCOSE-SPECIFIC PHOSPHOCARRIER


Theoretical massNumber of molelcules
Total (without water)36,2842
Polymers36,2842
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-11 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.040, 70.230, 74.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0515, -0.8642, -0.5006), (-0.9213, -0.1523, 0.3578), (-0.3855, 0.4796, -0.7883)
Vector: 24.41, 0.21, 62.81)
DetailsNONCRYSTALLOGRAPHIC SYMMETRY IS PROBABLY NOT BIOLOGICALLY RELEVANT.

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Components

#1: Protein GLUCOSE-SPECIFIC PHOSPHOCARRIER / EIIA-GLC


Mass: 18141.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: IIAGLC PROTEOLYZED-MISSING 16 N-TERMINAL AMINO ACIDS
Source: (natural) Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 8.5
Details: 30% PEG 4000, 0.2M MGCL2, 0.1M TRIS, PH 8.5 4 DEGREES
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
230 %mPEG40001reservoir
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 15616 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.036
Reflection
*PLUS
Num. measured all: 44614

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Processing

Software
NameVersionClassification
UNPUBLISHEDmodel building
TNT5Erefinement
SDMSdata reduction
SDMSdata scaling
UNPUBLISHEDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3G

1f3g


Resolution: 2.13→20 Å / Isotropic thermal model: TNT BCORREL V2.1 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.169 --
obs-15616 86 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.13→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 0 59 2334
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.011411221.5
X-RAY DIFFRACTIONt_angle_deg2.431043
X-RAY DIFFRACTIONt_dihedral_angle_d2114200
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009642
X-RAY DIFFRACTIONt_gen_planes0.023226
X-RAY DIFFRACTIONt_it6.323061.5
X-RAY DIFFRACTIONt_nbd0.0342310
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg210

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