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- PDB-7lgx: The aminoacrylate form of mutant beta-K167T Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7lgx
TitleThe aminoacrylate form of mutant beta-K167T Salmonella typhimurium Tryptophan Synthase in complex with with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, benzimidazole (BZI) at the enzyme beta site and cesium ion at the metal coordination site at 1.80 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-0JO / BENZIMIDAZOLE / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: The aminoacrylate form of mutant beta-K167T Salmonella typhimurium Tryptophan Synthase in complex with with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at ...Title: The aminoacrylate form of mutant beta-K167T Salmonella typhimurium Tryptophan Synthase in complex with with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, benzimidazole (BZI) at the enzyme beta site and cesium ion at the metal coordination site at 1.80 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionJan 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,48820
Polymers71,5902
Non-polymers1,89818
Water7,638424
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules

A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,97540
Polymers143,1794
Non-polymers3,79636
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15270 Å2
ΔGint-227 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.332, 60.080, 67.273
Angle α, β, γ (deg.)90.000, 94.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Tryptophan synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan synthase alpha chain


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42890.805 Da / Num. of mol.: 1 / Mutation: K167T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): K167T / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 442 molecules

#3: Chemical ChemComp-F9F / 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE, F9


Mass: 365.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11F3NO7PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BZI / BENZIMIDAZOLE


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.27 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 6 mM spermine, pH 7.6
PH range: 7.60-8.00 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.797→91.341 Å / Num. obs: 67106 / % possible obs: 98.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.55 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Rsym value: 0.089 / Net I/av σ(I): 4.1 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.96.60.540.66459397780.2530.6270.543.399.2
1.9-2.016.30.35415761892110.1790.420.3544.698.4
2.01-2.1560.2081.95190386120.1060.2490.2086.198.2
2.15-2.326.70.1635387580800.0750.1860.16899
2.32-2.556.70.1144.64986074670.050.1310.1149.599.5
2.55-2.856.40.0985.44278467270.0440.1120.09811.598.5
2.85-3.2970.0836.54180360130.0350.0940.08314.999.8
3.29-4.026.20.0775.63126050480.0350.0880.07717.498.6
4.02-5.6970.0589.22771339680.0250.0660.0582099.7
5.69-39.3146.50.0568.81426222020.0240.0640.05619.598.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.537
Highest resolutionLowest resolution
Rotation39.31 Å2 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 66455
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.35-10038.70.935519
6.75-9.3541.50.923800
5.55-6.7539.60.8821057
4.83-5.5535.20.9021227
4.33-4.8326.50.9221378
3.95-4.3324.70.9141523
3.66-3.9525.60.8941619
3.43-3.66240.9051732
3.24-3.4324.40.881865
3.07-3.2423.70.891980
2.93-3.0723.90.8772078
2.81-2.9324.90.8752170
2.7-2.8125.60.8662230
2.6-2.724.50.8362275
2.51-2.625.50.8512403
2.43-2.5125.10.8592515
2.36-2.4325.40.8762572
2.29-2.3627.80.8252635
2.23-2.2927.80.5022634
2.18-2.2329.80.7682714
2.12-2.1829.80.8012917
2.08-2.1230.90.6772844
2.03-2.0830.30.5022914
1.99-2.0334.10.6923013
1.95-1.9935.30.623120
1.91-1.9539.40.3322997
1.87-1.91420.2733096
1.84-1.8741.10.4653293
1.8-1.8444.90.6094335

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Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HPX

4hpx


Resolution: 1.8→39.31 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 3433 5.21 %
Rwork0.2007 62456 -
obs0.2025 65889 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.86 Å2 / Biso mean: 44.2913 Å2 / Biso min: 13.65 Å2
Refinement stepCycle: final / Resolution: 1.8→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 103 444 5371
Biso mean--44.37 43.39 -
Num. residues----653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.37051270.34032528265598
1.82-1.850.31571150.3262510262598
1.85-1.880.3941470.33182460260795
1.88-1.910.38381320.34812309244193
1.91-1.940.39091070.33182291239888
1.94-1.970.25571360.29612476261297
1.97-2.010.31681310.25812546267799
2.01-2.050.2621360.25142491262798
2.05-2.090.28221370.25662258239590
2.09-2.130.26421430.23452541268499
2.13-2.180.26871540.22652511266599
2.18-2.240.29141440.23372465260996
2.24-2.30.28411340.2312413254794
2.3-2.370.24861380.21122525266399
2.37-2.440.25281400.20782534267499
2.44-2.530.23381370.2062547268499
2.53-2.630.2571540.21022527268199
2.63-2.750.24341220.21192491261397
2.75-2.90.25811660.20792538270499
2.9-3.080.24031390.195825712710100
3.08-3.310.22091510.18125732724100
3.31-3.650.20621480.17252540268899
3.65-4.180.22721420.16032541268398
4.18-5.260.17381320.14682598273099
5.26-39.310.18581210.18452672279399
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)
14.42130.23630.27344.5509-0.92783.9550.69290.21880.3809-0.8658-0.54250.9728-0.091-0.6246-0.13560.44310.25230.00120.5601-0.16310.6567-53.9619-18.052422.0572
24.283-1.5882-1.91163.16090.45383.26370.66910.36140.8865-0.805-0.4085-0.6526-0.618-0.1511-0.23860.42360.120.17350.38760.04780.6358-39.2534-12.03823.3732
33.7943-1.656-0.74824.02020.61921.72420.2784-0.07410.0567-0.1891-0.29910.191-0.0994-0.26460.04140.1680.00280.00450.3053-0.01280.2321-41.8415-27.772526.7608
43.50590.1756-1.13235.61580.19042.94960.39620.8845-0.6533-0.8303-0.5583-0.0498-0.1083-0.51140.1150.44510.225-0.14560.5712-0.15730.5456-47.3814-32.186914.5445
57.85513.6040.01963.90520.75455.28970.30480.9662-0.6604-1.1761-0.48970.5903-0.0214-1.15970.13280.59770.2361-0.24740.7447-0.28830.858-55.6657-33.667713.7062
62.1239-0.68841.90750.2777-0.46442.1092-0.07170.47960.2673-0.3275-0.25490.0584-0.27170.16430.30381.48470.8838-0.38171.2589-0.16390.5617-52.7283-18.36626.7746
70.7306-1.1743-0.29932.4899-0.03230.58861.00620.87580.5719-0.7994-0.3753-0.1433-0.4127-0.01760.54741.37631.2307-0.03860.64160.22460.5651-48.7471-8.775412.8685
82-9.776922220.0425-16.4437-12.16762.0402-2.9082-9.96145.82064.84832.8480.91310.0349-0.190.81590.07841.0825-64.4001-16.22057.8447
91.5554-0.3206-0.32980.16840.15331.64870.12630.2624-0.1563-0.0544-0.08930.01810.0544-0.1858-0.03610.2245-0.0126-0.02970.1643-0.01140.2156-15.5434-44.32048.8599
101.4996-0.0225-2.44480.3249-0.76355.70561.09480.19390.83330.2270.01360.2062-2.597-0.893-0.46350.7680.21340.2340.48480.05320.4463-20.0177-28.93623.1023
111.95260.2341-0.39010.01950.28271.59920.0615-0.05060.1465-0.01060.00290.0067-0.06260.012-0.05980.1858-0.01730.0020.12160.00710.1624-6.0368-35.962819.639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A1 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 91 )A30 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 159 )A92 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 194 )A160 - 194
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 211 )A195 - 211
6X-RAY DIFFRACTION6chain 'A' and (resid 212 through 225 )A212 - 225
7X-RAY DIFFRACTION7chain 'A' and (resid 226 through 267 )A226 - 267
8X-RAY DIFFRACTION8chain 'A' and (resid 268 through 268 )A268
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 100 )B2 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 196 )B101 - 196
11X-RAY DIFFRACTION11chain 'B' and (resid 197 through 396 )B197 - 396

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