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- PDB-5g5z: S.pneumoniae ABC-transporter substrate binding protein FusA in co... -

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Basic information

Entry
Database: PDB / ID: 5g5z
TitleS.pneumoniae ABC-transporter substrate binding protein FusA in complex with kestose
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 / 1-kestose / Fructooligosaccharide ABC transporter substrate-binding protein FusA
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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)227,32517
Polymers224,9474
Non-polymers2,37813
Water20,8251156
1
B: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
C: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6428
Polymers112,4732
Non-polymers1,1696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-38.3 kcal/mol
Surface area38910 Å2
MethodPISA
2
D: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules

A: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6839
Polymers112,4732
Non-polymers1,2097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area4500 Å2
ΔGint-46.4 kcal/mol
Surface area39080 Å2
MethodPISA
3
A: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules

D: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6839
Polymers112,4732
Non-polymers1,2097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area4500 Å2
ΔGint-46.4 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.610, 127.820, 120.550
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9744, -0.0118, -0.2243), (0.0177, -0.9995, -0.0243), (-0.2239, -0.0276, 0.9742)-66.7697, -81.0857, 51.9618
2given(-0.8008, 0.5989, 0.0075), (0.598, 0.7988, 0.066), (0.0335, 0.0574, -0.9978)-27.4891, 10.2604, -25.6826
3given(-0.7768, -0.6016, -0.1861), (0.5993, -0.797, 0.0748), (-0.1933, -0.0534, 0.9797)-50.4846, 3.8369, 24.4661

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Components

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


Mass: 56236.637 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)-alpha-D-glucopyranose / 1-kestose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 1-kestose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2/a1-b2_b1-c2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLACKING THE FIRST 46 N-TERMINAL RESIDUES

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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: 2.75 Å3/Da / Density % sol: 49.76 % / Description: NONE
Crystal growpH: 5
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: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.01→70.14 Å / Num. obs: 140542 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G5Y

5g5y


Resolution: 2.01→70.145 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 6931 4.9 %
Rwork0.1681 --
obs0.1707 140533 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.71 Å2
Refinement stepCycle: LAST / Resolution: 2.01→70.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15788 0 145 1156 17089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116399
X-RAY DIFFRACTIONf_angle_d1.0222162
X-RAY DIFFRACTIONf_dihedral_angle_d16.5095996
X-RAY DIFFRACTIONf_chiral_restr0.132339
X-RAY DIFFRACTIONf_plane_restr0.0052886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.03280.32642440.28474355X-RAY DIFFRACTION99
2.0328-2.05680.33112270.27944415X-RAY DIFFRACTION99
2.0568-2.08190.30022250.25974476X-RAY DIFFRACTION99
2.0819-2.10820.29892190.25474396X-RAY DIFFRACTION99
2.1082-2.13590.32512570.24644440X-RAY DIFFRACTION99
2.1359-2.16520.30882480.22924433X-RAY DIFFRACTION100
2.1652-2.19610.27442170.21944404X-RAY DIFFRACTION99
2.1961-2.22890.29422370.21134429X-RAY DIFFRACTION100
2.2289-2.26380.26072310.20914401X-RAY DIFFRACTION100
2.2638-2.30090.25832230.2014453X-RAY DIFFRACTION100
2.3009-2.34060.27952550.1994430X-RAY DIFFRACTION100
2.3406-2.38310.27142290.19364421X-RAY DIFFRACTION100
2.3831-2.4290.2492450.18614470X-RAY DIFFRACTION100
2.429-2.47850.24582210.18164451X-RAY DIFFRACTION100
2.4785-2.53240.24862190.18194450X-RAY DIFFRACTION100
2.5324-2.59130.23472170.17634457X-RAY DIFFRACTION100
2.5913-2.65610.21522140.17364489X-RAY DIFFRACTION100
2.6561-2.7280.24782300.16964465X-RAY DIFFRACTION100
2.728-2.80820.24632520.1684445X-RAY DIFFRACTION100
2.8082-2.89890.21852390.16934396X-RAY DIFFRACTION100
2.8989-3.00250.24922120.16114496X-RAY DIFFRACTION100
3.0025-3.12270.21582240.15184485X-RAY DIFFRACTION100
3.1227-3.26480.22012140.1544468X-RAY DIFFRACTION100
3.2648-3.4370.18832480.14264472X-RAY DIFFRACTION100
3.437-3.65230.19192200.13934500X-RAY DIFFRACTION100
3.6523-3.93430.1822330.13654468X-RAY DIFFRACTION100
3.9343-4.33010.17322360.13144482X-RAY DIFFRACTION100
4.3301-4.95660.1692080.13474512X-RAY DIFFRACTION100
4.9566-6.24410.21392610.16934474X-RAY DIFFRACTION100
6.2441-70.18760.21542260.17984569X-RAY DIFFRACTION99

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