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

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Basic information

Entry
Database: PDB / ID: 1ble
TitlePHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM
ComponentsFRUCTOSE PERMEASE
KeywordsPHOSPHOTRANSFERASE / SUGAR TRANSPORT
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-fructose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system fructose-specific EIIB component
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å
AuthorsSchauder, S. / Schirmer, T.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the IIB subunit of a fructose permease (IIBLev) from Bacillus subtilis.
Authors: Schauder, S. / Nunn, R.S. / Lanz, R. / Erni, B. / Schirmer, T.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Levanase Operon of Bacillus Subtilis Includes a Fructose-Specific Phosphotransferase System Regulating the Expression of the Operon
Authors: Martin-Verstraete, I. / Debarbouille, M. / Klier, A. / Rapoport, G.
History
DepositionMay 15, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)18,2411
Polymers18,2411
Non-polymers00
Water1267
1
A: FRUCTOSE PERMEASE

A: FRUCTOSE PERMEASE

A: FRUCTOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)54,7233
Polymers54,7233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
Unit cell
Length a, b, c (Å)106.900, 106.900, 106.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein FRUCTOSE PERMEASE / FRUCTOSE TRANSPORTER / IIB SUBUNIT


Mass: 18241.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: WA2127 AND D41 / Gene: LEVE / Plasmid: PRL1 / Production host: Bacillus subtilis (bacteria)
References: UniProt: P26380, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-24 mg/mlprotein1drop
25 mMHEPES1drop
33.2-3.8 Msodium formate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 2, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 4889 / % possible obs: 97.7 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.288 / % possible all: 96.7
Reflection shell
*PLUS
% possible obs: 96.7 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: EXCEPT FOR THE ACTIVE LOOP RESIDUE PHE 13, ALL MAIN CHAIN ATOMS ARE WITHIN THE ALLOWED REGIONS OF THE RAMACHANDRAN PLOT.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 -10 %RANDOM
Rwork0.185 ---
obs0.185 4866 97.6 %-
Displacement parametersBiso mean: 64.5 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 0 7 1187
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.4
X-RAY DIFFRACTIONx_mcangle_it4.1
X-RAY DIFFRACTIONx_scbond_it3.3
X-RAY DIFFRACTIONx_scangle_it5.1
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.427 -10 %
Rwork0.289 532 -
obs--98.8 %
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_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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