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- PDB-7ki7: The external aldimine crystal structure of the beta-K167T mutant ... -

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Entry
Database: PDB / ID: 7ki7
TitleThe external aldimine crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.75 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / inhibitor / external aldimine / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / Tryptophan synthase beta subunit-like PLP-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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Chem-F9F / Chem-KOU / 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: 1.75 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 external aldimine crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.75 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate ...Title: The external aldimine crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.75 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionOct 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 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)73,57825
Polymers71,5902
Non-polymers1,98823
Water9,476526
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)147,15550
Polymers143,1794
Non-polymers3,97646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17190 Å2
ΔGint-344 kcal/mol
Surface area42230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.703, 59.419, 67.358
Angle α, β, γ (deg.)90.000, 94.720, 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 , 8 types, 549 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.56 Å3/Da / Density % sol: 52 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 8.0
PH range: 7.6-8.0 / 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: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→91.042 Å / Num. obs: 72171 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.05 / Rrim(I) all: 0.127 / Rsym value: 0.106 / Net I/av σ(I): 4.8 / Net I/σ(I): 10.5
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
1.75-1.846.40.712167751105090.3270.8380.7122.699.6
1.84-1.966.90.4881.46832699730.2170.5690.488499.7
1.96-2.096.80.3441.96335093580.1520.3980.3445.899.5
2.09-2.266.30.2562.35434486440.1190.2980.2567.999
2.26-2.476.90.1942.95564780580.0850.2240.19410.599.7
2.47-2.776.80.14544966872660.0640.1670.14513.199.6
2.77-3.26.20.1015.93979964070.0490.1220.10115.898.8
3.2-3.916.20.06793369954010.0330.0840.0672298.9
3.91-5.536.20.05510.62602042200.0270.0680.05525.799
5.53-29.7096.10.04612.41431423350.0210.0550.04625.397.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.439
Highest resolutionLowest resolution
Rotation29.71 Å1.96 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 72126
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.35-10030.50.925507
6.66-9.3535.20.918880
5.45-6.6638.20.9041046
4.73-5.4530.60.9181294
4.23-4.7325.30.9291467
3.86-4.2323.50.941629
3.58-3.8622.90.9351741
3.35-3.5822.60.931877
3.16-3.35240.9171969
3-3.1623.20.9142065
2.86-324.40.9112236
2.74-2.8623.70.9012291
2.63-2.7422.90.9162410
2.53-2.6322.20.9212507
2.45-2.5320.60.9312611
2.37-2.4520.50.9332677
2.3-2.3720.20.9282770
2.23-2.320.40.9232810
2.17-2.2320.10.9212892
2.12-2.1720.40.9253036
2.07-2.1221.30.9223071
2.02-2.0721.20.9173143
1.98-2.0221.60.9143188
1.94-1.9822.60.9053307
1.9-1.9422.90.9023357
1.86-1.923.20.9093406
1.82-1.8625.10.8933511
1.79-1.8227.30.8773560
1.75-1.7935.80.8164868

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.7.03phasing
DM7.0.078phasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.75→29.71 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 3659 5.07 %
Rwork0.1887 68461 -
obs0.1911 72120 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.97 Å2 / Biso mean: 33.1452 Å2 / Biso min: 3.27 Å2
Refinement stepCycle: final / Resolution: 1.75→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4937 0 96 556 5589
Biso mean--41.45 41.1 -
Num. residues----659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.32121380.29592615275399
1.77-1.80.34571330.26642621275499
1.8-1.820.27051360.253626332769100
1.82-1.850.26681130.23826612774100
1.85-1.880.30481150.23562648276399
1.88-1.910.2831410.222526082749100
1.91-1.940.26211390.2212625276499
1.94-1.980.26571430.220526422785100
1.98-2.020.26791460.22342611275799
2.02-2.060.26631570.20852609276699
2.06-2.10.24841520.19692611276399
2.1-2.150.2211390.19042621276099
2.15-2.20.23441260.19542658278499
2.2-2.260.23771520.18912553270598
2.26-2.330.24141510.183926262777100
2.33-2.410.21151420.185826682810100
2.41-2.490.22091460.184526452791100
2.49-2.590.22611320.185426492781100
2.59-2.710.23981370.195126562793100
2.71-2.850.26291530.19222597275099
2.85-3.030.22741460.18932637278399
3.03-3.260.21671480.18332573272197
3.26-3.590.21581340.16582678281299
3.59-4.110.21341420.16192643278599
4.11-5.170.22371570.15712669282699
5.18-29.710.23321410.19792704284597
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)
10.33060.3453-0.42640.6013-0.2830.73740.04870.03060.16630.2932-0.2144-0.1744-0.24750.169-0.00120.3316-0.0372-0.04090.26130.04920.396551.368812.236811.7672
20.76670.39980.61220.80580.1450.68830.00510.00430.4090.2766-0.07890.4057-0.2968-0.0442-0.10210.32670.02260.11320.1782-0.00140.458436.644218.133910.9057
31.07150.9675-0.28441.605-0.1190.36320.15850.05780.05440.0594-0.0883-0.0161-0.09760.0010.00040.1551-00.02520.17940.01330.20139.03522.65096.7826
41.01740.8529-0.24021.008-0.21970.24820.3576-0.4905-0.51880.861-0.6299-0.5691-0.25420.3239-0.33280.5189-0.1307-0.22130.32090.1040.454446.9457-2.080520.7005
50.69670.68870.11890.760.18690.83050.2769-0.18690.15690.5666-0.35250.0035-0.21470.07010.00250.5865-0.1071-0.06440.3135-0.01690.403547.98316.16122.3463
60.69060.12390.0380.1989-0.09380.76210.02-0.105-0.09690.0131-0.0307-0.02040.01460.0346-0.00010.13190.0077-0.0120.11020.0040.132412.1479-14.293824.5136
71.06690.2974-0.59550.99711.17832.30450.55370.16080.4222-0.2685-0.1351-0.0319-1.66970.10870.6760.65140.00410.15230.23020.02970.282616.55433.008931.283
80.64280.1709-0.06890.4079-0.19560.80630.02750.0242-0.03210.0013-0.021-0.02270.07140.0647-0.00010.13590.0112-0.00430.144-0.01340.12598.878-12.166217.5679
90.3801-0.417-0.0057-0.007-0.30740.09790.14120.1210.67190.0122-0.0627-0.2169-0.0340.0360.01320.13590.00190.03350.1810.04030.280216.75883.15799.197
100.2406-0.2515-0.07950.3938-0.07430.67430.06880.10020.0866-0.0309-0.0249-0.0195-0.0648-0.025800.1328-0.0007-0.00310.14550.00330.15832.5384-4.274412.1443
110.98910.4274-0.2520.3752-0.42611.19540.07530.01920.17140.10120.05290.0681-0.1501-0.03770.00120.15790.0170.02210.15040.0160.145-6.7081-2.383416.4337
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 202 )A160 - 202
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 268 )A203 - 268
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 100 )B2 - 100
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 180 )B101 - 180
8X-RAY DIFFRACTION8chain 'B' and (resid 181 through 269 )B181 - 269
9X-RAY DIFFRACTION9chain 'B' and (resid 270 through 301 )B270 - 301
10X-RAY DIFFRACTION10chain 'B' and (resid 302 through 343 )B302 - 343
11X-RAY DIFFRACTION11chain 'B' and (resid 344 through 396 )B344 - 396

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