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- PDB-7me8: The internal aldimine form of the wild-type Salmonella Typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7me8
TitleThe internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the beta-site, sodium ion at the metal coordination site and dual beta-Q114 rotamer conformation at 1.60 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / inhibitor / internal aldimine
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm
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-F6F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / 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: The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the beta-site, ...Title: The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the beta-site, sodium ion at the metal coordination site and dual beta-Q114 rotamer conformation at 1.60 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 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)72,3857
Polymers71,6182
Non-polymers7675
Water13,079726
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)144,77014
Polymers143,2354
Non-polymers1,53510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11540 Å2
ΔGint-34 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.404, 59.570, 67.279
Angle α, β, γ (deg.)90.000, 95.040, 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: 42918.879 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: trpB / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 731 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-F6F / 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE, F6


Mass: 329.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11F3NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 53.35 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 6, 2021 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.599→91.348 Å / Num. obs: 85682 / % possible obs: 90 % / Redundancy: 2.8 % / Biso Wilson estimate: 16.13 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.034 / Rrim(I) all: 0.059 / Rsym value: 0.042 / Net I/av σ(I): 8.5 / Net I/σ(I): 9.4
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
1.6-1.692.80.2363.128990104060.1890.3220.236375.3
1.69-1.792.90.1664.433875118540.1340.230.166490.7
1.79-1.912.80.1156.131405112620.0950.1620.1155.691.1
1.91-2.072.80.0798.42714198570.0650.1130.0798.486.2
2.07-2.262.80.076.42767498650.0580.0990.071193.3
2.26-2.532.80.04614.22435187680.0380.0670.04611.491.6
2.53-2.922.80.03515.82314281630.0290.0520.03513.696.3
2.92-3.582.80.02814.21967269700.0240.0420.02816.197.4
3.58-5.062.80.02515.51538254750.0210.0370.02517.998.1
5.06-39.3862.80.01915.8852930620.0160.0280.01917.197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.489
Highest resolutionLowest resolution
Rotation39.39 Å1.81 Å

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Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.6→39.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 4236 4.95 %
Rwork0.2101 81402 -
obs0.2119 85638 89.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.01 Å2 / Biso mean: 21.1174 Å2 / Biso min: 6.72 Å2
Refinement stepCycle: final / Resolution: 1.6→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 48 734 5610
Biso mean--23.46 28.63 -
Num. residues----645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.24031160.22612620273658
1.63-1.660.27362030.22543558376179
1.66-1.690.27192300.22654019424989
1.69-1.720.24462100.21744075428590
1.72-1.760.26482110.21694074428590
1.76-1.80.26092190.21574074429391
1.8-1.850.26512310.22444105433691
1.85-1.90.27672010.25554045424690
1.9-1.950.45731970.41013854405185
1.95-2.020.28792070.22543790399784
2.02-2.090.21222200.18644219443993
2.09-2.170.23711930.19144264445793
2.17-2.270.37372190.3424170438993
2.27-2.390.29612130.23043978419188
2.39-2.540.23212320.19384296452895
2.54-2.740.2222130.18414376458996
2.74-3.010.22272370.18724366460396
3.01-3.450.20952570.17634425468297
3.45-4.340.21252160.17234482469897
4.34-39.390.17722110.16274612482398
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)
12.0830.02330.39711.17290.16531.3920.1025-0.25230.26520.0274-0.0537-0.0721-0.14130.1241-0.03350.1692-0.02250.01020.1426-0.01240.179345.890714.984612.1515
21.86710.58860.14221.57070.39810.86440.0705-0.08720.1887-0.0242-0.09680.0709-0.1122-0.03890.03390.1202-0.0010.01740.0907-0.00050.116337.47687.31877.5221
32.3264-0.1127-0.16243.3284-0.0881.41710.1292-0.5288-0.40740.4265-0.0965-0.2930.23090.1672-0.02040.2341-0.0107-0.05680.2560.06540.242749.3359-5.299218.5676
40.9968-0.20050.3531.772-0.2220.90830.0323-0.25090.23110.3882-0.19790.0863-0.26050.03820.13230.2916-0.0717-0.02460.3115-0.06010.245348.351816.237321.9372
50.98390.18670.02980.8149-0.42141.26330.0021-0.0479-0.16290.0632-0.0418-0.1260.07060.21880.04110.11410.0098-0.00330.16570.01860.128227.7087-12.992919.5124
61.54810.21750.20690.37370.25241.06470.0173-0.03360.17170.0074-0.0178-0.0379-0.06860.12130.00050.1049-0.00350.00990.10120.02010.100511.0441-7.178828.3375
71.3261-0.1327-0.38630.2673-0.17570.73450.01920.03090.1528-0.02320.005-0.0183-0.05640.0289-0.01870.0953-0.007-0.01250.09170.00170.08176.9432-4.207411.3746
81.39380.51030.59610.758-0.03342.4689-0.00990.03280.19130.03090.04190.1039-0.3315-0.1614-0.02520.11030.02070.01740.10520.01360.0999-6.7977-3.573115.7443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )A1 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 159 )A62 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 202 )A160 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 267 )A203 - 267
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 37 )B2 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 220 )B38 - 220
7X-RAY DIFFRACTION7chain 'B' and (resid 221 through 343 )B221 - 343
8X-RAY DIFFRACTION8chain 'B' and (resid 344 through 394 )B344 - 394

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