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- PDB-6fmg: Structure of the Mannose Transporter IIA Domain from Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 6fmg
TitleStructure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae
ComponentsPTS system mannose-specific transporter subunit IIAB
KeywordsTRANSFERASE / PTS / mannose transporter
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane => GO:0016020 / plasma membrane / cytoplasm
Similarity search - Function
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 superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile.
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMagoch, M. / Grudnik, P.
CitationJournal: To Be Published
Title: Structure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae
Authors: Magoch, M. / Grudnik, P. / Nogly, P. / Dubin, G. / Archer, M. / Ma, P.
History
DepositionJan 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PTS system mannose-specific transporter subunit IIAB
B: PTS system mannose-specific transporter subunit IIAB
C: PTS system mannose-specific transporter subunit IIAB
D: PTS system mannose-specific transporter subunit IIAB


Theoretical massNumber of molelcules
Total (without water)60,1884
Polymers60,1884
Non-polymers00
Water8,323462
1
A: PTS system mannose-specific transporter subunit IIAB
D: PTS system mannose-specific transporter subunit IIAB


Theoretical massNumber of molelcules
Total (without water)30,0942
Polymers30,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-35 kcal/mol
Surface area11750 Å2
MethodPISA
2
B: PTS system mannose-specific transporter subunit IIAB
C: PTS system mannose-specific transporter subunit IIAB


Theoretical massNumber of molelcules
Total (without water)30,0942
Polymers30,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-38 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.528, 138.528, 69.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
PTS system mannose-specific transporter subunit IIAB


Mass: 15047.067 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: manL_2, ERS020456_01132 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0T8BTT4, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate 0.1 M Sodium cacodylate 6.5 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→49.15 Å / Num. obs: 1461081 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.5 % / Rmerge(I) obs: 2.052 / CC1/2: 0.666 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PDO

1pdo


Resolution: 1.8→26.179 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 3652 5.17 %
Rwork0.1702 67037 -
obs0.1716 70689 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.3 Å2 / Biso mean: 32.1307 Å2 / Biso min: 14.44 Å2
Refinement stepCycle: final / Resolution: 1.8→26.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 0 462 4662
Biso mean---38.7 -
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114276
X-RAY DIFFRACTIONf_angle_d1.0885788
X-RAY DIFFRACTIONf_chiral_restr0.065648
X-RAY DIFFRACTIONf_plane_restr0.007772
X-RAY DIFFRACTIONf_dihedral_angle_d11.0792584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82370.33661500.303725592709100
1.8237-1.84870.30891360.282925492685100
1.8487-1.87510.29191490.271625702719100
1.8751-1.90310.27111320.245525622694100
1.9031-1.93280.24331220.228625822704100
1.9328-1.96450.25751300.213325812711100
1.9645-1.99830.21121350.207325472682100
1.9983-2.03460.23981570.197125612718100
2.0346-2.07380.22361440.194925842728100
2.0738-2.11610.22851090.197625952704100
2.1161-2.16210.22521450.188225452690100
2.1621-2.21230.20961380.179225652703100
2.2123-2.26760.20691290.159425872716100
2.2676-2.32890.18911300.164325932723100
2.3289-2.39740.21031440.159525842728100
2.3974-2.47470.20781390.16825642703100
2.4747-2.56310.2041430.16525672710100
2.5631-2.66560.21781650.168125712736100
2.6656-2.78680.21791430.17825572700100
2.7868-2.93360.18841700.170925612731100
2.9336-3.11710.19811260.175725902716100
3.1171-3.35730.22861140.178426132727100
3.3573-3.69430.18991420.148126162758100
3.6943-4.2270.14451630.134825702733100
4.227-5.31820.14211420.12626292771100
5.3182-26.18210.1681550.17132635279099

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