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- PDB-5g5y: S.pneumoniae ABC-transporter substrate binding protein FusA apo s... -

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Basic information

Entry
Database: PDB / ID: 5g5y
TitleS.pneumoniae ABC-transporter substrate binding protein FusA apo structure
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 / Fructooligosaccharide ABC transporter substrate-binding protein FusA
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,07222
Polymers112,7012
Non-polymers1,37120
Water23,0591280
1
A: ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,26114
Polymers56,3511
Non-polymers91013
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)56,8118
Polymers56,3511
Non-polymers4617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.070, 72.170, 77.660
Angle α, β, γ (deg.)108.02, 104.99, 92.49
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0723, -0.9974, 0.002), (-0.9971, 0.0722, -0.0221), (0.0219, -0.0036, -0.9998)
Vector: 60.0329, 62.5278, -42.3242)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 56350.738 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 1300 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGENE NAME SP_1796 LACKING THE FIST 47 N-TERMINAL RESIDUES, PLUS GP RESIDUE ADDITION AFTER 3C PROTEASE CUT

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Description: A PARTIAL MODEL OF FUSA WAS OBTAINED BY FUSA-GFP CRYSTALS USING GFP AS STARTING MODEL FOR MOLECULAR REPLACEMENT
Crystal growpH: 8
Details: 15 % PEG6000, 0.1M TRIS-HCL PH 8.0, 0.01 M ZINC CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2552
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2552 Å / Relative weight: 1
ReflectionResolution: 1.73→68.01 Å / Num. obs: 114100 / % possible obs: 83.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.6 / % possible all: 33.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→70.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.422 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19317 5627 4.9 %RANDOM
Rwork0.16088 ---
obs0.16245 108465 83.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.943 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→70.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 49 1280 9261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198155
X-RAY DIFFRACTIONr_bond_other_d0.0020.027525
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.95111042
X-RAY DIFFRACTIONr_angle_other_deg0.952317409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32125.99419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.445151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3731520
X-RAY DIFFRACTIONr_chiral_restr0.0920.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021832
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_it1.6362.2333950
X-RAY DIFFRACTIONr_mcbond_other1.6242.2323949
X-RAY DIFFRACTIONr_mcangle_it2.473.344934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4332.4714205
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: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 159 -
Rwork0.38 3228 -
obs--33.76 %

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