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- PDB-1pdo: PHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM -

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Basic information

Entry
Database: PDB / ID: 1pdo
TitlePHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM
ComponentsMANNOSE PERMEASE
KeywordsPHOSPHOTRANSFERASE / PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / N-acetylglucosamine transport / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / N-acetylglucosamine transport / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / protein homodimerization activity / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / : / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component ...Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / : / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannose-specific EIIAB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS SOFTWARE USED : CCP4 PROGRAM SUITE 1994 STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 1.7 Å
AuthorsNunn, R.S. / Erni, B. / Schirmer, T.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure of the IIA domain of the mannose transporter from Escherichia coli at 1.7 angstroms resolution.
Authors: Nunn, R.S. / Markovic-Housley, Z. / Genovesio-Taverne, J.C. / Flukiger, K. / Rizkallah, P.J. / Jansonius, J.N. / Schirmer, T. / Erni, B.
#1: Journal: J.Biol.Chem. / Year: 1987
Title: The Mannose Permease of Escherichia Coli Consists of Three Different Proteins. Amino Acid Sequence and Function in Sugar Transport, Sugar Phosphorylation, and Penetration of Phage Lambda DNA
Authors: Erni, B. / Zanolari, B. / Kocher, H.P.
History
DepositionMar 8, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 21, 2020Group: Advisory / Data collection / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _pdbx_database_status.process_site / _reflns_shell.Rmerge_I_obs
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _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: MANNOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)14,6251
Polymers14,6251
Non-polymers00
Water1,26170
1
A: MANNOSE PERMEASE

A: MANNOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)29,2492
Polymers29,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3370 Å2
ΔGint-29 kcal/mol
Surface area10640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.360, 76.360, 88.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-181-

HOH

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Components

#1: Protein MANNOSE PERMEASE / MANNOSE TRANSPORTER / IIAB SUBUNIT


Mass: 14624.625 Da / Num. of mol.: 1
Fragment: IIA ==MAN== DOMAIN, RESIDUES 2 - 133, OF THE IIAB ==MAN== SUBUNIT PLUS PHE-ALA-GLY AT THE CARBOXY TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12-RP7029
Description: SUBCLONAL IIA COMPRISES RESIDUES 1 - 133 OF THE WILD-TYPE IIAB SEQUENCE PLUS PHE-ALA-GLY AT THE CARBOXY TERMINUS. THE INITIAL SE-MET WAS REMOVED BY PROTEOLYTIC CLEAVAGE.
Plasmid: PJFL1320 / Species (production host): Escherichia coli / Gene (production host): MANX / Production host: Escherichia coli K12 (bacteria) / Strain (production host): WA2127 AND D41
References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDURING CATALYSIS HIS 10 GETS TRANSIENTLY PHOSPHORYLATED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19.3 mg/mlprotein1dropand 9.8 mg/ml
21.8 Mammonium sulfate1reservoir
310 mM1reservoirCoCl2
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 3, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→19.8 Å / Num. obs: 16839 / % possible obs: 97.3 % / Observed criterion σ(I): 4 / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 8.1 / % possible all: 95.8
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS SOFTWARE USED : CCP4 PROGRAM SUITE 1994 STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Resolution: 1.7→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 -10 %
Rwork0.189 --
obs0.189 16645 95.8 %
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 0 70 1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it22
X-RAY DIFFRACTIONx_mcangle_it33
X-RAY DIFFRACTIONx_scbond_it33
X-RAY DIFFRACTIONx_scangle_it44
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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