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- PDB-5g60: S.pneumoniae ABC-transporter substrate binding protein FusA in co... -

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Basic information

Entry
Database: PDB / ID: 5g60
TitleS.pneumoniae ABC-transporter substrate binding protein FusA in complex with nystose
ComponentsABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / FUSA / SUBSTRATE-BINDING-PROTEIN / ABC-TRANSPORTER / TRANSPORTER / FRUCTOOLIGOSACCHARIDES / KESTOSE / NYSTOSE / FRUCTO-NYSTOSE / CARBOHYDRATE / SUGAR / TRANSPORT / PNEUMONIAE
Function / homologypolysaccharide transport / : / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / plasma membrane / nystose / Fructooligosaccharide ABC transporter substrate-binding protein FusA
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCulurgioni, S. / Harris, G. / Singh, A.K. / King, S.J. / Walsh, M.A.
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Regulation and Specificity of Fructooligosaccharide Import in Streptococcus pneumoniae.
Authors: Culurgioni, S. / Harris, G. / Singh, A.K. / King, S.J. / Walsh, M.A.
History
DepositionJun 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
B: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
C: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
D: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,79421
Polymers225,4034
Non-polymers3,39117
Water29,7251650
1
A: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1905
Polymers56,3511
Non-polymers8394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2256
Polymers56,3511
Non-polymers8745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1905
Polymers56,3511
Non-polymers8394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1905
Polymers56,3511
Non-polymers8394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 129.740, 120.280
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7928, -0.6082, 0.0397), (-0.6089, 0.7876, -0.0944), (0.0262, -0.099, -0.9947)83.1054, 36.85, 156.827
2given(0.9765, -0.002, 0.2156), (0.0026, -0.9998, -0.0214), (0.2156, 0.0214, -0.9762)-23.9596, 77.5198, 171.0283
3given(-0.7615, 0.6143, -0.2067), (-0.6184, -0.7841, -0.0518), (-0.1939, 0.0884, 0.977)62.6292, 95.5238, -21.1356

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN / FUSA


Mass: 56350.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: A0A0H2URD6
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / nystose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 666.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: nystose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2-2/a1-b2_b1-c2_c1-d2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1663 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1650 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsLACKING THE FIRST 47 N-TERMINAL AMINOACIDS

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8
Details: 20 % PEG6000, 0.1M SODIUM ACETATE PH 5.0, 0.02 M CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.99→57.37 Å / Num. obs: 144038 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.1 / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G5Y

5g5y


Resolution: 1.99→119.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.45 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22092 7120 4.9 %RANDOM
Rwork0.16928 ---
obs0.17183 136862 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.493 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.99→119.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15685 0 213 1650 17548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216340
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214935
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.96322097
X-RAY DIFFRACTIONr_angle_other_deg1.018334580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93251951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82625.932826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.783152762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2991540
X-RAY DIFFRACTIONr_chiral_restr0.0990.22347
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118467
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023633
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_it2.0942.7267838
X-RAY DIFFRACTIONr_mcbond_other2.0932.7257834
X-RAY DIFFRACTIONr_mcangle_it3.0414.0819763
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0112.9928502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 430 -
Rwork0.324 7992 -
obs--76.95 %

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