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- PDB-4rs3: Crystal structure of carbohydrate transporter A0QYB3 from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4rs3
TitleCrystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol
ComponentsABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / HYDROLASE
Function / homology
Function and homology information


cellular response to carbohydrate stimulus / carbohydrate transport / carbohydrate binding / plasma membrane
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Xylitol / Xylitol-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis.
Authors: Huang, H. / Carter, M.S. / Vetting, M.W. / Al-Obaidi, N. / Patskovsky, Y. / Almo, S.C. / Gerlt, J.A.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Structure summary
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,55737
Polymers34,6051
Non-polymers1,95136
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.841, 63.070, 73.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein / Periplasmic sugar-binding proteins


Mass: 34605.309 Da / Num. of mol.: 1 / Fragment: residues 25-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3598, MSMEI_3515 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QYB3, monosaccharide-transporting ATPase
#2: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O5

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Non-polymers , 5 types, 263 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growpH: 7
Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM DL-XYLITOL), RESERVOIR: 0.1 M IMIDAZOLE-HCL, PH 8.0, 0.2M ZINC ACETATE, 2.5M SODIUM CHLORIDE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR ...Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM DL-XYLITOL), RESERVOIR: 0.1 M IMIDAZOLE-HCL, PH 8.0, 0.2M ZINC ACETATE, 2.5M SODIUM CHLORIDE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 57826 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 21.085 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→47.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.934 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16294 1794 3.1 %RANDOM
Rwork0.124 ---
obs0.12524 55931 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0 Å2-0 Å2
2---0.34 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 73 228 2614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192425
X-RAY DIFFRACTIONr_bond_other_d0.0020.022362
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9953289
X-RAY DIFFRACTIONr_angle_other_deg1.02735448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.2427.525101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25715387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.549156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212838
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02490
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_it4.4161.8451280
X-RAY DIFFRACTIONr_mcbond_other4.1591.8321275
X-RAY DIFFRACTIONr_mcangle_it4.943.1051598
X-RAY DIFFRACTIONr_mcangle_other5.0263.1111599
X-RAY DIFFRACTIONr_scbond_it11.8572.7331145
X-RAY DIFFRACTIONr_scbond_other11.8542.7341146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.0894.1641686
X-RAY DIFFRACTIONr_long_range_B_refined8.8488.0182938
X-RAY DIFFRACTIONr_long_range_B_other8.8478.0212939
X-RAY DIFFRACTIONr_rigid_bond_restr7.37834787
X-RAY DIFFRACTIONr_sphericity_free31.607568
X-RAY DIFFRACTIONr_sphericity_bonded21.21754952
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 146 -
Rwork0.152 4054 -
obs--99.08 %

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