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- PDB-5mlt: Structural characterization of a carbohydrate substrate binding p... -

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Basic information

Entry
Database: PDB / ID: 5mlt
TitleStructural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae
ComponentsABC transporter, substrate-binding protein
KeywordsTRANSPORT PROTEIN / Substrate binding protein Carbohydrate periplasmic binding protein type 2 superfamily
Function / homology
Function and homology information


external side of cell wall / carbohydrate import across plasma membrane / protein homotrimerization / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein homotetramerization / protein homodimerization activity / zinc ion binding
Similarity search - Function
Domain of unknown function DUF3502 / Domain of unknown function (DUF3502) / : / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Carbohydrate ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.61 Å
AuthorsCulurgioni, S. / Tang, M. / Walsh, M.A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structural characterization of the Streptococcus pneumoniae carbohydrate substrate-binding protein SP0092.
Authors: Culurgioni, S. / Tang, M. / Walsh, M.A.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_symmetry / _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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4664
Polymers51,2691
Non-polymers1963
Water6,089338
1
A: ABC transporter, substrate-binding protein
hetero molecules

A: ABC transporter, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9318
Polymers102,5392
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15910 Å2
ΔGint-322 kcal/mol
Surface area42100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.240, 82.540, 60.350
Angle α, β, γ (deg.)90.00, 107.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ABC transporter, substrate-binding protein


Mass: 51269.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Gene: SP_0092 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UMY0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02 M Mes pH 6.5, 0.2 M NaCl, 2.5% glycerol and 0.5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2016 / Details: KB mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→49.64 Å / Num. obs: 62913 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.023 / Rsym value: 0.028 / Net I/av σ(I): 6.7 / Net I/σ(I): 16.4
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 4 / CC1/2: 0.578 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
xia2v1-3-4data reduction
Aimless0.5.29data scaling
SHELXCD2016/1phasing
RefinementMethod to determine structure: SAD / Resolution: 1.61→49.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.029 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22871 3158 5 %RANDOM
Rwork0.19292 ---
obs0.19469 59803 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 25.227 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.61→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 3 338 3924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023680
X-RAY DIFFRACTIONr_bond_other_d0.0020.023516
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9714990
X-RAY DIFFRACTIONr_angle_other_deg0.9338140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32626.648176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8515641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.735156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
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_it1.6612.3351823
X-RAY DIFFRACTIONr_mcbond_other1.6592.3351822
X-RAY DIFFRACTIONr_mcangle_it2.723.4962278
X-RAY DIFFRACTIONr_mcangle_other2.7193.4962279
X-RAY DIFFRACTIONr_scbond_it2.0812.5571857
X-RAY DIFFRACTIONr_scbond_other2.0812.5571857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4043.7132707
X-RAY DIFFRACTIONr_long_range_B_refined6.19219.3034326
X-RAY DIFFRACTIONr_long_range_B_other6.01319.0094213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å
RfactorNum. reflection% reflection
Rfree0.36 215 -
Rwork0.35 4436 -
obs--99.96 %

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