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- PDB-7ka1: 1.60 Angstrom resolution crystal structure of the beta-Q114A muta... -

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Entry
Database: PDB / ID: 7ka1
Title1.60 Angstrom resolution crystal structure of the beta-Q114A mutant Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Lyase / inhibitor / tryptophan synthase / 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 / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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: 1.60 Angstrom resolution crystal structure of the beta-Q114A mutant Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the ...Title: 1.60 Angstrom resolution crystal structure of the beta-Q114A mutant Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: 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)74,74938
Polymers71,5612
Non-polymers3,18936
Water13,115728
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tryptophan Synthase complex (alpha2-beta2) Protein is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-67 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.730, 60.890, 67.310
Angle α, β, γ (deg.)90.000, 94.850, 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: 42861.828 Da / Num. of mol.: 1 / Mutation: Q114A
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): beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 764 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#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-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.64 Å3/Da / Density % sol: 53.38 % / Description: Large plate like-crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 4 mM Spermine, pH 7.6
PH range: 7.60-8.00

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 5, 2020 / Details: Osmic Varimax HF ArcSec
RadiationMonochromator: Osmic Varimax HF ArcSec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→91.536 Å / Num. obs: 86059 / % possible obs: 88.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.041 / Rrim(I) all: 0.079 / Rsym value: 0.056 / Net I/av σ(I): 8.4 / Net I/σ(I): 10.1
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
1.6-1.693.50.262.537499105900.1860.3580.263.274.8
1.69-1.793.60.1843.540459112840.1320.2560.1844.484.1
1.79-1.913.50.134.938178108950.0940.1820.13686.4
1.91-2.073.40.0877.336283105180.0660.1270.0878.189.4
2.07-2.263.50.0718.83441198960.0540.1030.07110.691.4
2.26-2.533.60.0649.93321891070.0470.090.06412.593
2.53-2.923.80.0610.33072081630.0430.0840.0614.994.2
2.92-3.583.80.054112650470080.0380.0730.05418.295.5
3.58-5.063.80.03516.82072655080.0260.050.03520.496.6
5.06-29.3453.70.03614.31128030900.030.0560.03618.997

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.29 Å29.35 Å
Translation7.29 Å29.35 Å

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.6.1phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6d0v

6d0v


Resolution: 1.6→29.35 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 4274 4.97 %
Rwork0.1549 81691 -
obs0.1564 85965 87.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.65 Å2 / Biso mean: 23.3023 Å2 / Biso min: 9.44 Å2
Refinement stepCycle: final / Resolution: 1.6→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 168 776 5949
Biso mean--30.43 33.03 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.2621950.21971868196361
1.62-1.640.20981030.19742115221868
1.64-1.660.21291360.19022541267783
1.66-1.680.20731160.19252584270083
1.68-1.70.22041410.18982543268483
1.7-1.720.21811310.2032578270983
1.72-1.750.22681350.18722588272384
1.75-1.770.23121330.18222586271984
1.77-1.80.23551300.17342626275685
1.8-1.830.20771430.16872602274585
1.83-1.860.20891320.16672674280687
1.86-1.90.21011380.17072687282587
1.9-1.930.18021440.16542673281787
1.93-1.970.21141380.15942751288988
1.97-2.020.20161350.16592758289390
2.02-2.060.19171400.15892787292790
2.06-2.110.18381460.15442784293090
2.11-2.170.1721480.14712801294991
2.17-2.240.17511530.15022846299992
2.24-2.310.17881540.15092834298892
2.31-2.390.17281580.14942834299292
2.39-2.490.19421120.15162919303193
2.49-2.60.20571590.15742889304893
2.6-2.740.17811700.1562884305494
2.74-2.910.19411780.15672923310194
2.91-3.130.17351560.14952941309795
3.13-3.450.18221520.14292954310695
3.45-3.940.14511510.13413013316496
3.94-4.960.15881860.1312993317996
4.96-29.350.21981610.17193115327696
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)
15.03481.9065-0.52323.7464-0.5942.6335-0.01550.27920.1632-0.03350.11650.42190.02-0.5173-0.09840.16650.07010.03440.2518-0.02050.2524-54.3402-3.601521.5022
21.1467-0.3943-0.13141.2921-0.1270.79370.036-0.10730.14210.0335-0.01170.0416-0.1045-0.1058-0.02460.12990.01930.01770.1796-0.01840.1683-40.3749-6.385125.8503
34.89831.1044-1.67151.67680.46433.7194-0.02870.36-0.4213-0.04540.00860.02210.2026-0.2685-0.00780.14870.0475-0.04030.2049-0.01880.2401-46.0486-16.322313.7469
49.13776.0863-0.93646.62111.05062.315-0.56941.26260.2854-0.95320.47360.4182-0.0928-0.47010.04060.37510.0454-0.15540.4509-0.0380.4151-53.2185-16.90565.9814
51.93680.2560.13012.80170.2551.3620.08460.13930.2845-0.3361-0.14070.1554-0.247-0.2030.06760.23850.09250.00480.25430.02590.2451-48.73231.971611.9649
61.2643-0.4073-0.04080.4970.10591.42390.00910.0357-0.1631-0.0521-0.00560.08130.1716-0.22880.00060.1567-0.0457-0.00330.16750.00270.1538-30.3416-28.844314.1955
72.84570.4631.31940.87190.6932.32870.09440.1238-0.17310.0087-0.05270.00090.22280.0888-0.10920.13510.00960.01830.05920.00670.0878-2.9598-33.40985.9221
80.7097-0.17920.05420.3508-0.06450.73360.01620.02310.00450.0006-0.00610.02580.0045-0.0819-0.01690.145-0.0060.00050.1322-0.0050.1192-14.1577-22.5767.3628
91.3488-0.2091-0.080.1491-0.00630.91080.0309-0.09330.08850.0229-0.01620.0436-0.0347-0.0565-0.01630.1383-0.0070.00290.1297-0.00730.1188-14.5992-16.548725.052
100.9310.1011-0.39820.207-0.11090.91570.0055-0.01720.00110.0195-0.0129-0.0335-0.0070.05360.00140.12790.0019-0.00320.1077-0.0050.1214-2.7077-20.86520.8096
111.1237-0.59231.17861.592-1.15653.4611-0.02490.1250.1119-0.0238-0.0346-0.1379-0.23070.26370.0670.1003-0.01550.04040.1516-0.01580.10823.9599-18.710215.3383
122.3352.19852.00372.26132.02791.82381.49682.4215-1.8486.5435-1.89810.24090.65361.48930.4340.6075-0.08250.02560.2861-0.01130.3241-25.3993-4.137715.6879
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 159 )A30 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 187 )A160 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 202 )A188 - 202
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 268 )A203 - 268
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 37 )B2 - 37
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 70 )B38 - 70
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 244 )B71 - 244
9X-RAY DIFFRACTION9chain 'B' and (resid 245 through 301 )B245 - 301
10X-RAY DIFFRACTION10chain 'B' and (resid 302 through 364 )B302 - 364
11X-RAY DIFFRACTION11chain 'B' and (resid 365 through 395 )B365 - 395
12X-RAY DIFFRACTION12chain 'B' and (resid 426 through 426 )B426

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