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- PDB-7m2l: The internal aldimine form of the wild-type Salmonella Typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7m2l
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 1.60 Angstrom resolution. Two 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 / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / 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-F6F / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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 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 1.60 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionMar 16, 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

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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)73,25118
Polymers71,6182
Non-polymers1,63316
Water9,530529
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 area6390 Å2
ΔGint-48 kcal/mol
Surface area22780 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, 545 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: 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
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 529 / 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: 2.53 Å3/Da / Density % sol: 51.44 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-NaOH, 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 16, 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→91.385 Å / Num. obs: 92823 / % possible obs: 99.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 18.04 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.034 / Rrim(I) all: 0.061 / Rsym value: 0.043 / Net I/av σ(I): 9 / Net I/σ(I): 8.3
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
1.6-1.692.50.362231723127750.2930.4970.362294.1
1.69-1.792.90.2612.937199128760.1990.3550.261399.9
1.79-1.912.90.1734.235256121050.1350.240.1734.2100
1.91-2.0730.1136.133332112860.0880.1570.1136.4100
2.07-2.2630.0748.731020104100.0580.1040.0748.7100
2.26-2.5330.05311.22826694160.0420.0760.05310.599.9
2.53-2.9230.04115.52528083330.0320.0580.04113.199.9
2.92-3.583.10.03216.72176170580.0250.0450.03216.6100
3.58-5.063.10.02318.51691954830.0180.0330.02319.199.9
5.06-39.41130.02114.8936330810.0220.0370.02118.799.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.452
Highest resolutionLowest resolution
Rotation39.41 Å1.87 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 92809
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.67-10033.70.902622
6.13-8.67350.891121
5.01-6.1330.60.9051442
4.34-5.0122.20.9311677
3.88-4.3419.20.9391863
3.54-3.8820.40.9292106
3.28-3.54190.9292290
3.07-3.2818.70.9272422
2.89-3.0719.70.922581
2.74-2.8919.80.9182738
2.61-2.7419.20.9232856
2.5-2.6119.80.9183009
2.41-2.519.80.9213081
2.32-2.4118.80.933277
2.24-2.3218.70.923325
2.17-2.2418.70.9243474
2.1-2.1718.90.933602
2.04-2.119.10.9313682
1.99-2.0421.70.9223794
1.94-1.9921.40.9243848
1.89-1.9421.80.9244006
1.85-1.8923.20.9184071
1.81-1.8523.90.9154184
1.77-1.8125.90.9054221
1.73-1.7726.50.8994389
1.7-1.7328.70.8894413
1.67-1.730.90.8724478
1.64-1.6734.10.8484593
1.6-1.6443.10.7845644

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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: 4HT3

4ht3


Resolution: 1.6→39.41 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 4600 4.96 %
Rwork0.1744 88162 -
obs0.1757 92762 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.83 Å2 / Biso mean: 29.0871 Å2 / Biso min: 8.22 Å2
Refinement stepCycle: final / Resolution: 1.6→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 98 543 5552
Biso mean--32.48 35.83 -
Num. residues----660
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 (%)
1.6-1.620.39691270.31842384251182
1.62-1.640.31631660.3072703286991
1.64-1.660.32061510.29022849300098
1.66-1.680.32621760.27229743150100
1.68-1.70.31191430.258329053048100
1.7-1.720.26291600.245330023162100
1.72-1.750.25051430.234629103053100
1.75-1.770.24541590.23429603119100
1.77-1.80.26911600.22729123072100
1.8-1.830.26551630.212929573120100
1.83-1.860.24261610.206629763137100
1.86-1.90.20331440.196229633107100
1.9-1.930.21421460.187529393085100
1.93-1.970.22651470.190830153162100
1.97-2.020.22931580.197329393097100
2.02-2.060.23031430.192829413084100
2.06-2.110.18631470.171330023149100
2.11-2.170.23071380.168529893127100
2.17-2.240.20241640.173329523116100
2.24-2.310.20951550.173729603115100
2.31-2.390.19431570.164929433100100
2.39-2.490.18791730.174729673140100
2.49-2.60.22581380.167129823120100
2.6-2.740.18651470.164729643111100
2.74-2.910.18211660.164929913157100
2.91-3.130.18991740.168329553129100
3.13-3.450.17661630.160629973160100
3.45-3.940.17751400.142430063146100
3.94-4.970.15021470.129230213168100
4.97-39.410.17361440.160931043248100
Refinement TLS params.Method: refined / Origin x: 21.315 Å / Origin y: -0.6101 Å / Origin z: 17.6366 Å
111213212223313233
T0.1527 Å2-0.0154 Å2-0.0074 Å2-0.1293 Å2-0.0139 Å2--0.151 Å2
L1.1389 °20.1952 °2-0.6834 °2-0.4635 °2-0.2442 °2--0.9178 °2
S0.1419 Å °-0.1413 Å °0.1478 Å °0.0783 Å °-0.0696 Å °-0.116 Å °-0.1638 Å °0.2134 Å °-0.0478 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 267
2X-RAY DIFFRACTION1allA301 - 401
3X-RAY DIFFRACTION1allB2 - 396
4X-RAY DIFFRACTION1allB501 - 1101
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allD1 - 529
7X-RAY DIFFRACTION1allE1 - 5

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