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- PDB-4n4d: Structure of ThiT with AV-38 bound -

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Basic information

Entry
Database: PDB / ID: 4n4d
TitleStructure of ThiT with AV-38 bound
Componentsthiamine binding protein ThiT
KeywordsTHIAMINE BINDING PROTEIN/INHIBITOR / S-component / ECF transporter / ABC transporter / transport protein / THIAMINE BINDING PROTEIN-INHIBITOR complex
Function / homologyArp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-XX8 / :
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSwier, L.J.Y.M. / Guskov, A. / Slotboom, D.J.
CitationJournal: To be Published
Title: Structural studies on the thiamine binding protein ThiT
Authors: Swier, L.J.Y.M. / Gomez, L. / Guskov, A. / Hirsch, A.K.H. / Slotboom, D.J.
History
DepositionOct 8, 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 / 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 binding protein ThiT
B: thiamine binding protein ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,17632
Polymers39,8482
Non-polymers5,32830
Water82946
1
A: thiamine binding protein ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,98319
Polymers19,9241
Non-polymers3,05918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: thiamine binding protein ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,19313
Polymers19,9241
Non-polymers2,26912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.160, 84.260, 127.250
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 7 molecules AB

#1: Protein thiamine binding protein ThiT


Mass: 19924.027 Da / Num. of mol.: 2 / Fragment: UNP residues 7-182
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.: 5
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, 71 molecules

#2: Chemical ChemComp-XX8 / {3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol


Mass: 229.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N3O
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 4.39 Å3/Da / Density % sol: 71.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15 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: ID23-1 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→42.304 Å / Num. all: 25938 / Num. obs: 25926 / % possible obs: 98.9 % / Observed criterion σ(F): 2
Reflection shellHighest resolution: 2.4 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: 2.4→42.304 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 1296 5 %
Rwork0.2044 --
obs0.2071 25926 99.26 %
all-25938 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→42.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 360 46 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143171
X-RAY DIFFRACTIONf_angle_d1.484208
X-RAY DIFFRACTIONf_dihedral_angle_d19.9721276
X-RAY DIFFRACTIONf_chiral_restr0.077466
X-RAY DIFFRACTIONf_plane_restr0.008452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.35641420.2892704X-RAY DIFFRACTION99
2.4961-2.60970.34241440.27082728X-RAY DIFFRACTION100
2.6097-2.74730.38091440.24212738X-RAY DIFFRACTION100
2.7473-2.91940.29421440.21832739X-RAY DIFFRACTION99
2.9194-3.14470.23491430.21022707X-RAY DIFFRACTION99
3.1447-3.4610.19611440.17112748X-RAY DIFFRACTION100
3.461-3.96150.28531430.18222720X-RAY DIFFRACTION99
3.9615-4.98990.23821450.17252749X-RAY DIFFRACTION99
4.9899-42.31080.22471470.22662797X-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)
17.78691.9262-0.83545.2324-6.52829.553-0.4479-1.209-0.62260.8506-0.9204-1.63620.3480.99231.28420.54890.04010.17060.68380.06370.43832.72233.000255.3128
29.1453-4.61664.19519.8248-6.95975.109-0.0782-1.15320.31321.76560.5730.0476-1.5392-0.5618-0.38220.85370.01520.0330.4083-0.07340.582227.54121.399243.1215
32.69211.0357-0.11996.87610.17184.3082-0.2479-0.3667-0.23781.14680.1583-0.1749-0.03250.04190.06520.38650.0737-0.07720.41150.05140.338326.66853.681650.9388
48.1495-3.838-3.37538.22223.61056.8091-0.0621-0.40390.49590.52950.0046-0.2185-0.4611-0.22140.12380.46380.01390.02250.31620.06320.367718.573710.622250.6132
55.9969-3.87250.90333.8748-4.14269.17230.30530.0389-1.03440.2105-0.48721.37560.49910.31370.27770.80960.05860.03670.38910.02620.729433.0062-9.5338.1109
66.7423-5.9789-0.90589.73730.90762.74560.1819-0.2693-0.4842-0.2116-0.18550.6942-0.1065-0.34410.00120.3006-0.04670.01330.31330.01940.386818.79288.925740.0775
76.2667-3.6074-1.36776.5122-1.42514.04810.23290.1930.5903-0.1183-0.0201-0.1396-0.6438-0.1543-0.19960.4585-0.0359-0.0610.2652-0.03250.398523.612616.535237.8784
89.6212-1.4631-6.37050.26671.02844.3032-0.4742-1.0751-1.72931.58230.2112-1.52951.51821.40750.27830.8560.1931-0.28460.50610.02740.756139.6116-3.79542.3195
92.83912.26741.35929.4845-1.26331.3643-0.7478-0.7408-0.98711.8786-0.2133-1.84851.95640.808-0.13651.87490.94010.15970.1410.29360.957937.5104-13.382449.1755
105.7031-1.32122.00265.4016-4.65924.6832-0.64731.08220.2016-1.9353-0.4689-1.28880.24440.43451.06340.5816-0.02510.08330.77420.04390.572537.215519.80737.6101
114.30663.93671.54089.6248-1.86962.8993-0.42990.7719-0.7404-1.32780.0146-0.71781.09150.37750.33750.73580.00070.17510.376-0.12040.583931.4661.530420.521
120.9198-1.3591-0.4453.8786-0.75284.9525-0.36950.2296-0.0911-0.47690.2337-0.6339-0.0040.00640.10970.3264-0.14260.04510.47460.03490.447931.100119.16211.9807
138.25574.4312.36083.76583.40916.934-0.02510.4029-0.7916-0.8379-0.1078-1.12820.3945-0.41860.11970.5987-0.0710.00640.34540.01620.413622.84812.380912.4235
145.29675.95057.02316.69887.85939.3148-0.39960.21090.52940.15520.11881.2434-0.61560.42610.34740.8214-0.1218-0.0650.45530.0250.690237.14233.848223.7656
154.65864.78893.90919.04781.31955.15690.0363-0.1708-0.0516-0.1865-0.1185-0.4009-0.3927-0.1510.03710.2790.00120.0230.3681-0.00210.443323.457914.960523.0808
167.03595.0448-4.36364.9866-5.21095.8461-0.4886-0.04-0.4384-0.4847-0.0964-0.38730.5501-0.50520.56090.7703-0.1212-0.00760.3199-0.00770.766717.2184-4.209923.5587
173.60951.9607-1.08915.0588-2.6985.402-0.11290.0457-0.31690.0973-0.3942-1.1231-0.31430.67030.48290.38560.0039-0.05940.34780.03910.555833.911114.068725.3608
186.51594.9036-0.45145.9727-1.08290.2696-1.5771.4190.6759-2.1838-0.10330.2161-1.49620.76170.66571.7048-0.7199-0.38920.60120.12031.142942.171136.273513.5901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 107 )
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 132 )
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 177 )
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 182 )
10X-RAY DIFFRACTION10chain 'B' and (resid 7 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 38 )
12X-RAY DIFFRACTION12chain 'B' and (resid 39 through 69 )
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 98 )
14X-RAY DIFFRACTION14chain 'B' and (resid 99 through 106 )
15X-RAY DIFFRACTION15chain 'B' and (resid 107 through 132 )
16X-RAY DIFFRACTION16chain 'B' and (resid 133 through 142 )
17X-RAY DIFFRACTION17chain 'B' and (resid 143 through 177 )
18X-RAY DIFFRACTION18chain 'B' and (resid 178 through 182 )

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