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

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Basic information

Entry
Database: PDB / ID: 7lvx
TitleThe internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.55 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / Inhibitor / internal aldimine
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan metabolic process / 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-F9F / 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'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha- ...Title: The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.55 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: 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)73,79425
Polymers71,6182
Non-polymers2,17623
Water13,583754
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 area7320 Å2
ΔGint-230 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.103, 59.088, 67.160
Angle α, β, γ (deg.)90.000, 94.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-413-

CS

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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 , 7 types, 777 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-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.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#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-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.85 Å3/Da / Density % sol: 51.43 % / 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: 7.60-8.0 / 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: Nov 23, 2020 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.549→90.774 Å / Num. obs: 97591 / % possible obs: 94.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.031 / Rrim(I) all: 0.055 / Rsym value: 0.034 / Net I/av σ(I): 10.3 / Net I/σ(I): 15
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
1.55-1.6320.0917.821757106360.0870.1360.0916.571.1
1.63-1.732.90.0838.439553136350.0680.120.0839.496.2
1.73-1.8530.06310.538772130040.0540.0960.06311.797.4
1.85-230.04912.536623121990.0440.0770.04914.498.3
2-2.1930.0415.934407113700.0360.0650.0416.798.9
2.19-2.4530.03517.531378103200.0320.0580.03518.499.5
2.45-2.833.10.031182818391840.030.0540.03119.899.8
2.83-3.473.10.031192405377820.0270.0490.03121.4100
3.47-4.93.10.0320.11881460690.0250.0450.0322.6100
4.9-29.54430.02911.61034333920.0290.0510.02922.399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.374
Highest resolutionLowest resolution
Rotation29.55 Å1.72 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 97514
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.4-100300.905683
5.94-8.439.50.8991222
4.85-5.9434.10.8981579
4.2-4.85260.9291844
3.76-4.226.60.9192095
3.43-3.7625.20.9272297
3.18-3.4326.50.9272514
2.97-3.1826.90.9182686
2.8-2.9727.50.9112829
2.66-2.825.50.923015
2.53-2.6625.50.9293180
2.43-2.5326.10.9213289
2.33-2.4324.20.9323396
2.25-2.3324.20.9323562
2.17-2.2523.10.9273649
2.1-2.17230.943779
2.04-2.122.90.9323859
1.98-2.0423.20.9234007
1.93-1.9823.30.9224138
1.88-1.9324.10.9144188
1.83-1.8824.20.9114276
1.79-1.8324.40.9084349
1.75-1.7924.40.9054471
1.71-1.7524.70.9044545
1.68-1.7125.40.8924594
1.65-1.68280.8774742
1.62-1.6528.60.8814487
1.59-1.6229.70.8653916
1.55-1.5936.20.8424323

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Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.55→29.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.848 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0908 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4962 5.1 %RANDOM
Rwork0.1431 ---
obs0.1455 92552 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 208.01 Å2 / Biso mean: 17.127 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.03 Å2
2--0.07 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.55→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 82 776 5840
Biso mean--25.49 31.34 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125314
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6337213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78822.374257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1115870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2581533
X-RAY DIFFRACTIONr_chiral_restr0.0960.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024111
X-RAY DIFFRACTIONr_rigid_bond_restr9.3135313
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 215 -
Rwork0.131 4437 -
all-4652 -
obs--61.18 %
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)
10.0812-0.1245-0.27160.23060.46360.9647-0.00450.012-0.00530.0199-0.0013-0.0010.0318-0.02130.00580.01820.00230.00230.01120.00080.019652.5459-2.457325.2683
20.0321-0.00720.02610.0285-0.01670.0286-0.0024-0.00670.00010.00430.002-0.0032-0.0013-0.00150.00040.01670.00030.00140.00830.00010.018147.925316.168122.3202
30.06950.0042-0.00480.00030.00040.05250.0009-0.0043-0.0004-0-0.00020.00080.00120.0017-0.00070.01740.00020.00040.00030.00010.019812.4658-14.319724.6939
40.045-0.0136-0.02040.0111-0.00980.04690.00020.0073-0.00110.0019-0.0018-0.0017-0.0026-0.00550.00150.0161-0.0003-0.00060.011-0.00040.018415.09332.98332.7851
50.04590.0098-0.04230.0027-0.00990.0419-0.0014-0.0096-0.0007-0.002-0.00160.00020.00030.00740.0030.01730.0007-0.00050.00280.00020.020312.8699-11.439621.1862
60.07540.0240.00310.0227-0.01490.0171-0.00170.00750.0048-0.00010.0008-0-0.00060.00290.00090.01800.00030.0033-0.00070.018211.8811-0.08768.935
70.1836-0.0547-0.0560.04090.01660.06750.0019-0.00240.003-0.0014-0.0001-0.0021-0.0018-0.0046-0.00180.0169-0.0007-0.00040.000700.01742.5206-4.32812.486
80.10840.0159-0.0090.05260.05880.0930.0042-0.00510.0071-0.005-0.0051-0.0012-0.0078-0.01580.00090.01750.00150.00040.00680.00030.0194-6.3511-2.831516.431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A188 - 202
2X-RAY DIFFRACTION2A203 - 268
3X-RAY DIFFRACTION3B2 - 100
4X-RAY DIFFRACTION4B101 - 165
5X-RAY DIFFRACTION5B166 - 244
6X-RAY DIFFRACTION6B245 - 301
7X-RAY DIFFRACTION7B302 - 343
8X-RAY DIFFRACTION8B344 - 394

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