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- PDB-5hko: Crystal structure of ABC transporter Solute Binding Protein MSMEG... -

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Basic information

Entry
Database: PDB / ID: 5hko
TitleCrystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol
ComponentsABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein
KeywordsSOLUTE-BINDING PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
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
L-glucitol / ACETATE ION / IMIDAZOLE / Xylitol-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRoth, Y. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
CitationJournal: To be published
Title: Crystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol
Authors: Roth, Y. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)38,66034
Polymers36,6551
Non-polymers2,00533
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.947, 62.940, 73.153
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36654.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)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

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Non-polymers , 6 types, 320 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-62W / L-glucitol / L-sorbitol / D-gulitol


Mass: 182.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O6
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-sorbitol); Reservoir (MCSG4 A7)(0.2 M Zinc Acetate Dihydrate, 0.1 M Imidazole pH 8, 2.5 M Sodium Chloride); Cryoprotection (20% Diethylene Glycol, 80% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 20, 2015 / 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: 1.2→50 Å / Num. obs: 91508 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Χ2: 1.262 / Net I/av σ(I): 24.165 / Net I/σ(I): 8.8 / Num. measured all: 650580
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.2470.68590210.8290.2770.741.03799.7
1.24-1.297.10.55790470.8790.2230.6011.049100
1.29-1.357.20.43790540.9220.1750.4711.089100
1.35-1.427.20.34690750.9460.1370.3721.139100
1.42-1.517.30.24790870.9720.0980.2661.237100
1.51-1.637.30.17690840.9850.070.191.255100
1.63-1.797.30.13791400.9890.0550.1481.441100
1.79-2.0570.11291810.9930.0460.1211.419100
2.05-2.5970.07692220.9960.0310.0821.442100
2.59-506.60.05495970.9970.0230.0581.5199.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RS3

4rs3


Resolution: 1.2→47.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.963 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 4465 4.9 %RANDOM
Rwork0.1558 ---
obs0.1568 86963 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.35 Å2 / Biso mean: 14.242 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2---0.21 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.2→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 73 287 2668
Biso mean--17.65 25.26 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.022436
X-RAY DIFFRACTIONr_bond_other_d0.0020.022376
X-RAY DIFFRACTIONr_angle_refined_deg2.8281.9833302
X-RAY DIFFRACTIONr_angle_other_deg1.213.0015478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.93827.327101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05115416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.529157
X-RAY DIFFRACTIONr_chiral_restr0.1680.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212854
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02501
X-RAY DIFFRACTIONr_mcbond_it1.2730.8731284
X-RAY DIFFRACTIONr_mcbond_other1.2420.8691280
X-RAY DIFFRACTIONr_mcangle_it1.8331.311608
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 340 -
Rwork0.213 6333 -
all-6673 -
obs--99.7 %
Refinement TLS params.Method: refined / Origin x: -3.9217 Å / Origin y: -23.338 Å / Origin z: 1.9355 Å
111213212223313233
T0.0085 Å20.0017 Å20.001 Å2-0.0185 Å2-0.001 Å2--0.0025 Å2
L0.582 °20.2019 °2-0.0234 °2-0.5282 °20.0687 °2--0.1709 °2
S-0.0177 Å °0.029 Å °-0.0068 Å °0.0058 Å °0.0235 Å °0.0155 Å °0.0152 Å °0.01 Å °-0.0058 Å °

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