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- PDB-5g61: S.pneumoniae ABC-transporter substrate binding protein FusA in co... -

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Basic information

Entry
Database: PDB / ID: 5g61
TitleS.pneumoniae ABC-transporter substrate binding protein FusA in complex with fructo-nystose
ComponentsABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / FUSA / SUBSTRATE-BINDING-PROTEIN / ABC-TRAN 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-FRUCTOFURANOSYL-D-NYSTOSE / Fructooligosaccharide ABC transporter substrate-binding protein FusA
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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)229,03816
Polymers225,4034
Non-polymers3,63612
Water19,8891104
1
A: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2604
Polymers56,3511
Non-polymers9093
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)57,2604
Polymers56,3511
Non-polymers9093
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)57,2604
Polymers56,3511
Non-polymers9093
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)57,2604
Polymers56,3511
Non-polymers9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.370, 135.910, 121.190
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9921, -0.0222, 0.1235), (-0.0216, -0.9997, -0.0061), (0.1236, 0.0034, -0.9923)-18.7391, -33.5752, 283.6768
2given(0.6033, -0.7911, 0.1011), (-0.7899, -0.6102, -0.0609), (0.1098, -0.0431, -0.993)56.3674, 147.2563, 252.7584
3given(0.6236, 0.7815, -0.0183), (-0.7816, 0.6229, -0.0322), (-0.0138, 0.0344, 0.9993)100.861, 165.4766, -29.638

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Components

#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)-beta-D- ...beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-sorbofuranose-(2-1)-beta-L-talopyranose / 1-FRUCTOFURANOSYL-D-NYSTOSE


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 828.719 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-FRUCTOFURANOSYL-D-NYSTOSE
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-1DSorfb2-1LTalpbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2221h-1b_1-5][ha212h-2b_2-5][ha122h-2b_2-5]/1-2-3-3-3/a1-b2_b1-c2_c1-d2_d1-e2WURCSPDB2Glycan 1.1.0
[][b-D-Sorf]{[(2+1)][b-L-Talp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.86 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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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: 2.4→90.37 Å / Num. obs: 95973 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 30.53 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.4 / % possible all: 99.8

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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: 2.4→90.37 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 4729 4.9 %
Rwork0.1856 --
obs0.1889 95932 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.4→90.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15784 0 232 1104 17120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01816479
X-RAY DIFFRACTIONf_angle_d1.05722282
X-RAY DIFFRACTIONf_dihedral_angle_d14.389738
X-RAY DIFFRACTIONf_chiral_restr0.0522365
X-RAY DIFFRACTIONf_plane_restr0.0052878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.34881720.26913005X-RAY DIFFRACTION100
2.4273-2.45580.34151610.26543046X-RAY DIFFRACTION100
2.4558-2.48580.34261810.25572978X-RAY DIFFRACTION100
2.4858-2.51730.29811530.25933045X-RAY DIFFRACTION100
2.5173-2.55040.34081540.24933060X-RAY DIFFRACTION100
2.5504-2.58530.32511620.253011X-RAY DIFFRACTION100
2.5853-2.62230.31621500.24753045X-RAY DIFFRACTION100
2.6223-2.66140.31231620.23943016X-RAY DIFFRACTION100
2.6614-2.7030.30231490.2333054X-RAY DIFFRACTION100
2.703-2.74730.31241510.23823047X-RAY DIFFRACTION100
2.7473-2.79470.30221360.22633022X-RAY DIFFRACTION100
2.7947-2.84550.32911570.22043063X-RAY DIFFRACTION99
2.8455-2.90020.30711430.21853038X-RAY DIFFRACTION99
2.9002-2.95940.27231790.21093028X-RAY DIFFRACTION100
2.9594-3.02380.28711560.19353007X-RAY DIFFRACTION100
3.0238-3.09410.30381730.18753025X-RAY DIFFRACTION100
3.0941-3.17150.24671390.17743084X-RAY DIFFRACTION100
3.1715-3.25730.28111420.17863013X-RAY DIFFRACTION100
3.2573-3.35310.24041680.17043066X-RAY DIFFRACTION100
3.3531-3.46140.22791650.16593045X-RAY DIFFRACTION100
3.4614-3.58510.21641640.15783033X-RAY DIFFRACTION100
3.5851-3.72860.2171650.15493031X-RAY DIFFRACTION100
3.7286-3.89830.19491830.15413032X-RAY DIFFRACTION100
3.8983-4.10380.2171540.15493054X-RAY DIFFRACTION99
4.1038-4.3610.22151560.14723011X-RAY DIFFRACTION99
4.361-4.69770.20811630.15283021X-RAY DIFFRACTION99
4.6977-5.17040.22671260.1573086X-RAY DIFFRACTION99
5.1704-5.91840.20931670.17323059X-RAY DIFFRACTION99
5.9184-7.4560.23241400.19053076X-RAY DIFFRACTION99
7.456-90.43390.21411580.18443102X-RAY DIFFRACTION99

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