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- PDB-1a3a: CRYSTAL STRUCTURE OF IIA MANNITOL FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1a3a
TitleCRYSTAL STRUCTURE OF IIA MANNITOL FROM ESCHERICHIA COLI
ComponentsMANNITOL-SPECIFIC EII
KeywordsPHOSPHOTRANSFERASE / PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM / IIA ENZYMES / HISTIDINE PHOSPHORYLATION
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannitol phosphotransferase / sorbitol transmembrane transport / protein-N(PI)-phosphohistidine-mannitol phosphotransferase system transmembrane transporter activity / protein-phosphocysteine-mannitol phosphotransferase system transporter activity / mannitol transmembrane transport / protein-phosphocysteine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / plasma membrane
Similarity search - Function
Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / : / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 ...Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / : / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannitol-specific EIICBA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTIPLE ANOMALOUS DISPERSION / Resolution: 1.8 Å
AuthorsVan Montfort, R.L.M. / Pijning, T. / Kalk, K.H. / Hangyi, I. / Kouwijzer, M.L.C.E. / Robillard, G.T. / Dijkstra, B.W.
CitationJournal: Structure / Year: 1998
Title: The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site.
Authors: van Montfort, R.L. / Pijning, T. / Kalk, K.H. / Hangyi, I. / Kouwijzer, M.L. / Robillard, G.T. / Dijkstra, B.W.
History
DepositionJan 19, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: MANNITOL-SPECIFIC EII
B: MANNITOL-SPECIFIC EII
C: MANNITOL-SPECIFIC EII
D: MANNITOL-SPECIFIC EII


Theoretical massNumber of molelcules
Total (without water)65,3944
Polymers65,3944
Non-polymers00
Water10,233568
1
A: MANNITOL-SPECIFIC EII
C: MANNITOL-SPECIFIC EII


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-6 kcal/mol
Surface area12960 Å2
MethodPISA
2
B: MANNITOL-SPECIFIC EII
D: MANNITOL-SPECIFIC EII


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.570, 66.010, 73.860
Angle α, β, γ (deg.)90.00, 99.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9997, -0.0072, -0.024), (-0.0092, 0.9963, 0.0859), (0.0233, 0.0861, -0.996)-4.6046, -38.3075, 33.2669
2given(-0.9209, -0.1001, -0.3768), (0.1857, -0.9625, -0.198), (-0.3428, -0.2523, 0.9049)31.5075, 74.4228, 10.4433
3given(0.9227, 0.0668, 0.3796), (0.1277, -0.9822, -0.1375), (0.3637, 0.1753, -0.9149)-36.0041, 37.1877, 29.2043

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Components

#1: Protein
MANNITOL-SPECIFIC EII


Mass: 16348.547 Da / Num. of mol.: 4 / Fragment: IIA DOMAIN, RESIDUES 491 - 637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: MTLA / Production host: Escherichia coli (E. coli)
References: UniProt: P00550, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 1.9 Å3/Da / Density % sol: 36.4 %
Description: MAD DATA WERE COLLECTED AT THE BM14 AT THE ESRF, GRENOBLE
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5 mg/mlprotein1drop
210 mMTris-HCl1drop
3150 mM1dropNaCl
41 mMNa2 EDTA1drop
51 mM1dropNaN3
636-38 %(w/v)PEG40001reservoir
70.1 mMTaps-NaOH1reservoir
85 mMNa2 EDTA1reservoir
91 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 45271 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.262 / % possible all: 84.2
Reflection
*PLUS
Num. measured all: 195844
Reflection shell
*PLUS
% possible obs: 84.2 %

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MULTIPLE ANOMALOUS DISPERSION
Resolution: 1.8→5 Å / Cross valid method: THROUGHOUT
Rfactor% reflectionSelection details
Rfree0.242 5 %RANDOM
Rwork0.19 --
obs0.19 --
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 0 568 5041
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.185 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.4

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