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- PDB-5t3u: Crystal Structure of the PTS IIA protein associated with the fuco... -

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Basic information

Entry
Database: PDB / ID: 5t3u
TitleCrystal Structure of the PTS IIA protein associated with the fucose utilization operon from Streptococcus pneumoniae
ComponentsPTS system, IIA component
KeywordsTRANSPORT PROTEIN / PTS / transport
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane
Similarity search - Function
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, IIA component
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHiggins, M.A. / Boraston, A.B.
CitationJournal: Proteins / Year: 2017
Title: Structural characterization of the PTS IIA and IIB proteins associated with pneumococcal fucose utilization.
Authors: Higgins, M.A. / Hamilton, A.M. / Boraston, A.B.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Mar 6, 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

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Assembly

Deposited unit
A: PTS system, IIA component
B: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7924
Polymers32,7332
Non-polymers3,0602
Water5,134285
1
A: PTS system, IIA component
hetero molecules

A: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7924
Polymers32,7332
Non-polymers3,0602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area3880 Å2
ΔGint-32 kcal/mol
Surface area12320 Å2
MethodPISA
2
B: PTS system, IIA component
hetero molecules

B: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7924
Polymers32,7332
Non-polymers3,0602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_765-x+2,-y+1,z1
Buried area3590 Å2
ΔGint-26 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.202, 100.202, 192.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21B-378-

HOH

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Components

#1: Protein PTS system, IIA component


Mass: 16366.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_2164 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2US38
#2: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 15% PEG3350, 0.2M ammonium sulfate, 0.1M citrate pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 197784 / % possible obs: 95.2 % / Redundancy: 7.67 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CrystalCleardata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.45 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25277 1286 5 %RANDOM
Rwork0.20371 ---
obs0.20615 24508 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.741 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.15→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 29 285 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9622885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16226.132106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.215358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.824158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7781.51331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47622151
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1543804
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7084.5734
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 79 -
Rwork0.312 1788 -
obs--96.34 %

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