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- PDB-4muu: Structure of ThiT with pyrithiamine bound -

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Basic information

Entry
Database: PDB / ID: 4muu
TitleStructure of ThiT with pyrithiamine bound
ComponentsThiamine transporter ThiT
KeywordsTHIAMINE BINDING PROTEIN / S-component / ECF transporter / ABC transporter
Function / homologyArp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha / Chem-218 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / :
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSwier, L.J.Y.M. / Guskov, A. / Slotboom, D.J.
CitationJournal: To be Published
Title: Structural studies on the thiamin binding protein ThiT
Authors: Swier, L.J.Y.M. / Gomez, L. / Guskov, A. / Hirsch, A.K.H. / Slotboom, D.J.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Thiamine transporter ThiT
B: Thiamine transporter ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,88843
Polymers42,4632
Non-polymers7,42541
Water1,982110
1
A: Thiamine transporter ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,62123
Polymers21,2311
Non-polymers3,38922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiamine transporter ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,26720
Polymers21,2311
Non-polymers4,03619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.560, 84.590, 127.260
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-217-

PE5

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Thiamine transporter ThiT / Thiamine ECF transporter S component ThiT


Mass: 21231.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: NZ9000 / Gene: LLNZ_01755 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: D8KFM5
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 9 types, 148 molecules

#2: Chemical ChemComp-218 / 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-HYDROXYETHYL)-2-METHYLPYRIDINIUM


Mass: 259.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N4O
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.3 M ammonium nitrate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→42.217 Å / Num. all: 37975 / Num. obs: 37536 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Net I/σ(I): 2
Reflection shellHighest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RLB

3rlb


Resolution: 2.1→42.217 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 1876 5 %
Rwork0.1939 --
obs0.196 37528 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 501 110 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123309
X-RAY DIFFRACTIONf_angle_d1.4094341
X-RAY DIFFRACTIONf_dihedral_angle_d20.1221347
X-RAY DIFFRACTIONf_chiral_restr0.081471
X-RAY DIFFRACTIONf_plane_restr0.007459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.26691370.21812608X-RAY DIFFRACTION95
2.1568-2.22030.24081400.21862669X-RAY DIFFRACTION97
2.2203-2.29190.28671430.23742704X-RAY DIFFRACTION97
2.2919-2.37380.24731450.18922747X-RAY DIFFRACTION99
2.3738-2.46890.26411440.18012736X-RAY DIFFRACTION100
2.4689-2.58120.22591440.17772751X-RAY DIFFRACTION100
2.5812-2.71730.24681450.17522753X-RAY DIFFRACTION100
2.7173-2.88750.23651470.17432781X-RAY DIFFRACTION100
2.8875-3.11040.2341450.17682767X-RAY DIFFRACTION100
3.1104-3.42320.21761460.17842765X-RAY DIFFRACTION100
3.4232-3.91830.21681460.1822768X-RAY DIFFRACTION100
3.9183-4.93540.21091450.18872769X-RAY DIFFRACTION100
4.9354-42.22560.2641490.22812834X-RAY DIFFRACTION99
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)
15.57670.8275-0.3444.0897-5.29627.9315-0.1239-0.8326-0.42490.8922-0.23710.00270.55820.51050.35750.33420.09640.08350.45880.05170.207729.9782.523955.2864
22.8616-0.038-0.83023.42850.11824.9256-0.0888-0.3152-0.06370.40530.0867-0.0279-0.14610.1795-0.02710.19610.05190.0010.2470.00420.157924.442910.557148.4979
32.288-2.5195-0.75.82482.98464.8117-0.3422-0.5210.04780.86620.42410.1101-0.01690.01740.0260.25530.05610.06620.25750.01610.187716.164512.277150.4467
49.3162-5.6281-6.57027.6467.11767.0250.1561-0.7683-0.3056-0.16440.06210.07931.15810.46550.07450.35830.14560.00160.34680.02480.36830.1656-8.749538.3659
58.814-6.5494-3.67358.42934.07323.66610.0570.1222-0.1192-0.0664-0.16350.6117-0.2433-0.37730.06190.16490.03730.03670.19190.02430.190617.102610.158839.5992
63.3874-0.5333-1.22023.6005-0.64732.92140.04480.21030.54160.3152-0.0442-0.1822-0.4532-0.0437-0.04950.2362-0.01790.00960.1618-0.03040.142323.183415.708238.2372
77.6075-2.8539.02217.2341-2.9132.0026-1.0949-1.1212-0.90531.098-0.0896-0.05390.36620.61230.86410.93410.39420.03240.60980.14850.585234.4055-11.952649.1051
83.3008-0.04340.07128.2521-6.06224.4928-0.340.6537-0.0353-0.854-0.3611-1.2857-0.07590.57710.64320.5207-0.16970.05990.57510.02820.238836.370820.93327.4697
92.20710.7588-0.30432.8947-1.04324.2974-0.19060.4388-0.074-0.44070.2249-0.22980.18860.2733-0.04530.2553-0.08650.06970.2954-0.03870.232629.826414.374414.7634
102.83261.37721.13895.65161.6665.4441-0.20960.5865-0.0724-0.57840.23190.04220.5287-0.02050.01830.2751-0.03530.04880.27830.02480.167521.753412.573212.1948
113.3891.14491.64451.90063.72027.42090.5890.0440.2874-0.38620.61070.726-0.81180.5887-0.52450.577-0.1705-0.06160.3040.12960.407534.904534.650323.4488
128.92686.882.18468.82971.05533.9224-0.05130.0709-0.10710.00820.0544-0.0243-0.33330.0512-0.00460.2048-0.04120.05340.1754-0.0020.16721.794515.63722.905
132.57810.5705-1.63166.5499-3.51232.60150.20680.0274-1.2758-0.72080.075-0.3151.0503-0.5574-0.06530.458-0.1761-0.11170.28980.03760.470115.4322-3.488923.872
144.14533.0342-0.80376.2479-2.60853.6995-0.3339-0.2855-0.1713-0.3364-0.1995-0.5655-0.15250.46390.42130.2178-0.01-0.00910.1683-0.0160.183331.779114.81725.5286
150.079-0.8279-0.0738.0330.66870.054-0.44480.77380.7586-1.28020.2743-0.644-0.81080.54870.04390.7348-0.8387-0.29460.45820.9481.000540.15236.922713.3462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 187 )
7X-RAY DIFFRACTION7chain 'A' and (resid 188 through 192 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 36 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 108 )
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 116 )
12X-RAY DIFFRACTION12chain 'B' and (resid 117 through 142 )
13X-RAY DIFFRACTION13chain 'B' and (resid 143 through 152 )
14X-RAY DIFFRACTION14chain 'B' and (resid 153 through 187 )
15X-RAY DIFFRACTION15chain 'B' and (resid 188 through 192 )

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