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- PDB-7m3s: The internal aldimine form of the wild-type Salmonella Typhimuriu... -

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Entry
Database: PDB / ID: 7m3s
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 alpha-and beta-site, sodium ion at the metal coordination site, and another F6F molecule at the enzyme beta-site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / inhibitor / internal aldimine form / LYASE / LYASE-LYASE INHIBITOR complex
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: 1.55 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 alpha-and ...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 alpha-and beta-site, sodium ion at the metal coordination site, and another F6F molecule at the enzyme beta-site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionMar 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 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)73,25918
Polymers71,6182
Non-polymers1,64116
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tryptophan Synthase complex (alpha2-beta2). TS is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-27 kcal/mol
Surface area22700 Å2
MethodPISA
2
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)146,51836
Polymers143,2354
Non-polymers3,28232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17040 Å2
ΔGint-62 kcal/mol
Surface area41810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.518, 58.598, 67.098
Angle α, β, γ (deg.)90.000, 95.180, 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 , 8 types, 566 molecules

#3: 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.: 2 / Source method: obtained synthetically / Formula: C10H11F3NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.83 Å3/Da / Density % sol: 51.42 % / 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: 7.60-8.00 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 18, 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: 1.55→91.018 Å / Num. obs: 100288 / % possible obs: 95.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Rsym value: 0.039 / Net I/av σ(I): 12.6 / Net I/σ(I): 14.6
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
1.55-1.632.30.1464.925796111550.1410.2220.1463.973.8
1.63-1.733.30.135.547461141710.10.1870.135.998.6
1.73-1.853.50.0967.546586134490.0750.1420.096899.4
1.85-23.50.0710.144063125890.0560.1060.0711.499.8
2-2.193.60.05212.641306116320.0440.0830.05215.3100
2.19-2.453.60.0411637661105110.0360.0690.04118.999.9
2.45-2.833.60.03618.23387393310.0320.0620.03622100
2.83-3.473.70.03319.12899678770.0280.0540.03326.799.9
3.47-4.93.70.02722.42273161390.0230.0450.02731.499.9
4.9-39.1153.60.02819.21248934340.0280.0540.02829.999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.393
Highest resolutionLowest resolution
Rotation39.12 Å1.72 Å

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Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.55→39.41 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 4966 5.03 %
Rwork0.1769 93816 -
obs0.1781 98782 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.26 Å2 / Biso mean: 29.2848 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1.55→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 100 564 5578
Biso mean--34.48 35.21 -
Num. residues----661
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 (%)
1.55-1.570.3515860.33721846193257
1.57-1.590.29851030.3122179228266
1.59-1.610.32091200.31262420254075
1.61-1.630.34491390.30512822296186
1.63-1.650.3321660.28973040320694
1.65-1.670.29051630.266632523415100
1.67-1.690.28191800.253631783358100
1.69-1.720.27111890.233232813470100
1.72-1.750.25321590.228232103369100
1.75-1.770.26481470.225332743421100
1.77-1.80.25741840.215532063390100
1.8-1.840.24271850.207832463431100
1.84-1.870.23691560.197132863442100
1.87-1.910.19361620.191132443406100
1.91-1.950.21621900.185132403430100
1.95-20.21621730.189332493422100
2-2.050.1941820.194632603442100
2.05-2.10.23191960.176832143410100
2.1-2.170.21431640.171332853449100
2.17-2.240.21321770.170632513428100
2.24-2.320.17531900.17432023392100
2.32-2.410.21091640.169933053469100
2.41-2.520.1971600.174832473407100
2.52-2.650.19741950.167632573452100
2.65-2.820.21671670.172832793446100
2.82-3.030.17621500.176433043454100
3.03-3.340.18552040.163632443448100
3.34-3.820.17491890.144632763465100
3.82-4.810.15351480.128233443492100
4.81-39.410.15371780.156133753553100
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)
12.8185-0.72410.56322.47310.01812.11690.5037-0.41950.8432-0.0271-0.1895-0.8297-0.47050.8093-0.18030.2748-0.1630.0330.4406-0.0030.488551.36811.98411.736
23.16860.8431-0.65442.6305-0.36072.19380.3025-0.25330.41890.1164-0.2074-0.0952-0.41740.2303-0.0460.1774-0.05770.05640.1851-0.01890.215838.1659.468.911
35.3846-1.2312-1.19172.8923-2.07833.03620.2004-1.2602-0.3210.4114-0.3528-0.0695-0.26230.58660.15270.283-0.1347-0.10480.54220.10510.396443.968-1.70419.616
44.3516-3.1869-1.12576.09971.55150.5992-0.2728-1.3968-0.34151.07630.1599-0.33240.60890.82140.00820.37390.0048-0.24380.81160.1910.76752.738-5.05121.489
51.40560.084-0.03531.6853-0.46421.29740.1252-1.12140.47640.68650.1859-0.3377-0.52580.3975-0.13810.5028-0.21-0.08450.7327-0.22010.475446.49514.30724.04
62.62380.04560.19972.2331-0.09050.36170.0033-0.69010.67290.4050.0461-0.5341-0.7110.2787-0.02760.8042-0.3605-0.04670.6061-0.22470.602547.67621.03220.048
71.39760.2936-0.39621.1085-0.72892.12750.028-0.17-0.27280.0583-0.1383-0.21770.15520.57280.08260.11750.041-0.01720.23390.03040.174627.584-12.93819.543
82.1527-0.84140.61291.6186-1.0742.53760.1031-0.1371-0.2130.0218-0.0633-0.0490.1865-0.0481-0.06270.1434-0.00550.00610.0735-0.01190.10682.835-17.79829.876
92.27370.63370.28860.41590.22061.59570.0691-0.123-0.11040.02-0.0262-0.03930.0013-0.0908-0.03020.13930.0074-0.01260.04760.0070.09432.603-12.4124.921
102.27110.7418-1.05851.5278-0.1372.43180.2669-0.0950.45750.1178-0.07350.0116-0.49230.2447-0.15160.2246-0.06950.04270.1714-0.02250.183714.3992.87732.58
111.19250.3198-0.36572.59420.70952.57250.1685-0.24180.25670.11790.0297-0.3859-0.32220.5184-0.14430.1381-0.0619-0.00280.243-0.02060.192324.243-1.65225.839
121.90320.2311-0.53010.2295-0.20981.20770.01990.11960.0804-0.03270.0159-0.020.0003-0.0039-0.03090.10840.0197-0.00640.0753-0.00870.07378.43-8.13313.361
131.7925-0.3527-0.92480.40680.12551.34550.06210.08970.1562-0.01680.0082-0.0007-0.1445-0.0982-0.07970.11690.0137-0.00860.09090.01750.0912.49-4.23512.308
141.64950.61880.25341.3064-0.03022.90860.03340.06390.21730.0380.06780.1102-0.2734-0.2427-0.03360.10940.04270.03060.12310.02870.1072-6.82-3.61515.525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:29 )A1 - 29
2X-RAY DIFFRACTION2( CHAIN A AND RESID 30:159 )A30 - 159
3X-RAY DIFFRACTION3( CHAIN A AND RESID 160:187 )A160 - 187
4X-RAY DIFFRACTION4( CHAIN A AND RESID 188:207 )A188 - 207
5X-RAY DIFFRACTION5( CHAIN A AND RESID 208:247 )A208 - 247
6X-RAY DIFFRACTION6( CHAIN A AND RESID 248:267 )A248 - 267
7X-RAY DIFFRACTION7( CHAIN B AND RESID 2:37 )B2 - 37
8X-RAY DIFFRACTION8( CHAIN B AND RESID 38:66 )B38 - 66
9X-RAY DIFFRACTION9( CHAIN B AND RESID 67:100 )B67 - 100
10X-RAY DIFFRACTION10( CHAIN B AND RESID 101:165 )B101 - 165
11X-RAY DIFFRACTION11( CHAIN B AND RESID 166:196 )B166 - 196
12X-RAY DIFFRACTION12( CHAIN B AND RESID 197:301 )B197 - 301
13X-RAY DIFFRACTION13( CHAIN B AND RESID 302:343 )B302 - 343
14X-RAY DIFFRACTION14( CHAIN B AND RESID 344:394 )B344 - 394

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