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- PDB-4ry8: Crystal structure of 5-methylthioribose transporter solute bindin... -

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Basic information

Entry
Database: PDB / ID: 4ry8
TitleCrystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from Thermotoga lettingae TMO TARGET EFI-511109 in complex with 5-methylthioribose
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 5-S-methyl-5-thio-alpha-D-ribofuranose / Periplasmic binding protein/LacI transcriptional regulator
Function and homology information
Biological speciesThermotoga lettingae TMO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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. / Siede, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of 5-methylthioribose binding protein TLET_1677 from Thermotoga lettingae TARGET EFI-511109
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al obaidi, N. / Chamala, S. / Scott glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Morisco, L.L. / Wasserman, S.R. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al obaidi, N. / Chamala, S. / Scott glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Morisco, L.L. / Wasserman, S.R. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Periplasmic binding protein
B: Periplasmic binding protein
C: Periplasmic binding protein
D: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0748
Polymers146,3534
Non-polymers7214
Water8,575476
1
A: Periplasmic binding protein
C: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5374
Polymers73,1772
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-23 kcal/mol
Surface area24380 Å2
MethodPISA
2
B: Periplasmic binding protein
D: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5374
Polymers73,1772
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-22 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.622, 67.848, 83.653
Angle α, β, γ (deg.)91.83, 92.39, 89.93
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999996, 0.000352, -0.002893), (0.000376, -0.999965, 0.008405), (-0.00289, -0.008406, -0.99996)0.01663, 65.3016, 21.83962
3given(-0.999996, 0.000311, 0.002959), (-0.000344, -0.999941, -0.010893), (0.002955, -0.010894, 0.999936)97.93922, 65.5398, 0.27788
4given(-1, 0.000197, -0.000738), (0.000197, 1, -0.000356), (0.000738, -0.000356, -1)97.90417, -0.02871, 21.37169

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Components

#1: Protein
Periplasmic binding protein


Mass: 36588.270 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 22-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga lettingae TMO (bacteria) / Gene: Tlet_1677 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8F7U7
#2: Sugar
ChemComp-SR1 / 5-S-methyl-5-thio-alpha-D-ribofuranose / 5-S-methyl-5-thio-alpha-D-ribose / 5-S-methyl-5-thio-D-ribose / 5-S-methyl-5-thio-ribose


Type: D-saccharide, alpha linking / Mass: 180.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O4S
IdentifierTypeProgram
a-D-Ribf5SMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT); RESERVOIR: 0.1 M HEPES-NAOH, PH 7.5, 0.2 M MAGNESIUM CHLORIDE, 30% PPG P400; 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: Nov 22, 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: 1.75→50 Å / Num. obs: 128230 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 10
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 94.9

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.196 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26356 3771 3 %RANDOM
Rwork0.21444 ---
obs0.21593 119981 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.26 Å2
Baniso -1Baniso -2Baniso -3
1--3.67 Å2-0.31 Å2-0.41 Å2
2---3.8 Å20.37 Å2
3---7.44 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9868 0 44 476 10388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01910127
X-RAY DIFFRACTIONr_bond_other_d0.0010.029979
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.96613733
X-RAY DIFFRACTIONr_angle_other_deg0.835322888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36851276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48424.695443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.933151776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3691568
X-RAY DIFFRACTIONr_chiral_restr0.0910.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022191
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_it5.6721.5225104
X-RAY DIFFRACTIONr_mcbond_other5.6651.5225103
X-RAY DIFFRACTIONr_mcangle_it6.1822.2216371
X-RAY DIFFRACTIONr_mcangle_other6.1842.2216372
X-RAY DIFFRACTIONr_scbond_it10.8562.4885023
X-RAY DIFFRACTIONr_scbond_other10.8552.4885024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.1813.2467360
X-RAY DIFFRACTIONr_long_range_B_refined11.6425.56411857
X-RAY DIFFRACTIONr_long_range_B_other11.6425.56411858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 291 -
Rwork0.335 8540 -
obs--93.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.51880.0897-0.21011.7457-0.10160.4295-0.0096-0.1745-0.23150.19760.00730.00880.0346-0.02490.00220.26530.02240.01950.23410.03880.025248.995815.766228.1799
22.4017-0.42060.2551.6949-0.1380.4197-0.01290.18950.2358-0.17960.00020.0092-0.0276-0.01830.01270.2694-0.00980.02660.23720.04560.032448.290349.7741-7.1626
32.16310.37770.2751.60650.16990.4329-0.008-0.18460.21580.1688-0.0033-0.0321-0.03490.01640.01130.26450.02570.02560.23940.00780.032349.594949.629528.5266
42.2903-0.1055-0.11951.90080.22590.4334-0.00120.1888-0.2433-0.21630.0181-0.08530.02070.0387-0.01690.2708-0.0040.02590.24570.00520.036549.4815.5388-7.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 327
2X-RAY DIFFRACTION2B7 - 327
3X-RAY DIFFRACTION3C5 - 327
4X-RAY DIFFRACTION4D7 - 327

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