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- PDB-7lkl: The internal aldimine form of the wild-type Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7lkl
TitleThe internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 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 / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-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 / 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 / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / TRYPTOPHAN / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 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 inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the ...Title: The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 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
DepositionFeb 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 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)75,33840
Polymers71,6182
Non-polymers3,72038
Water15,133840
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)150,67580
Polymers143,2354
Non-polymers7,44076
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22220 Å2
ΔGint-315 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.741, 59.810, 67.299
Angle α, β, γ (deg.)90.000, 94.650, 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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA, DD95_04145 / Plasmid: pBR322 / Details (production host): pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: A0A0D6FWC1, 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 enterica subsp. enterica serovar Typhimurium (bacteria)
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 , 9 types, 878 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.55 Å3/Da / Density % sol: 51.88 % / 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: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.88558 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88558 Å / Relative weight: 1
ReflectionResolution: 1.05→90.571 Å / Num. obs: 312765 / % possible obs: 93.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.076 / Rrim(I) all: 0.146 / Rsym value: 0.115 / Net I/av σ(I): 3.7 / Net I/σ(I): 4.5
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
1.05-1.113.91.0310.4170925443620.6431.2631.0311.591.5
1.11-1.173.80.6080.8163029424290.3850.7560.6082.292.4
1.17-1.253.80.4091.3154224402480.2630.5160.4092.893.4
1.25-1.363.80.2871.8144579379200.190.3710.2873.594.3
1.36-1.483.80.1893133348352100.1270.2470.1894.695.2
1.48-1.663.80.1234.6121105321310.0840.1630.123695.9
1.66-1.923.70.096.4105938286500.0620.120.097.396.8
1.92-2.353.60.076.888100244070.0490.0930.078.497.6
2.35-3.323.80.0599.972591190010.0390.0750.0599.197.7
3.32-28.9043.30.0688.52800984070.0450.0830.0688.677.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.595
Highest resolutionLowest resolution
Rotation28.91 Å1.27 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 312736
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.69-10047.90.8341432
4.02-5.6941.10.8892958
3.29-4.0234.80.9144345
2.85-3.2928.50.9335727
2.55-2.8527.50.9246631
2.32-2.5527.20.9257268
2.15-2.3227.30.9317907
2.01-2.1528.40.9318386
1.9-2.0130.30.9188949
1.8-1.933.80.9119393
1.72-1.835.50.9069860
1.64-1.7238.80.90710313
1.58-1.6440.10.88510622
1.52-1.5841.40.8911072
1.47-1.5243.40.87911448
1.42-1.4745.80.85811742
1.38-1.42460.85212135
1.34-1.3847.80.83812430
1.31-1.3448.40.83212722
1.27-1.3150.20.81813040
1.24-1.2752.50.79213335
1.21-1.2453.60.78413564
1.19-1.2155.40.77513836
1.16-1.1958.20.76414104
1.14-1.1661.10.74314330
1.12-1.1462.60.73214613
1.1-1.1268.10.71714852
1.08-1.173.10.6814980
1.05-1.0884.60.61320742

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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: 5cgq

5cgq


Resolution: 1.05→28.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.239 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 15524 5 %RANDOM
Rwork0.1545 ---
obs0.1556 297211 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.06 Å2 / Biso mean: 12.923 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0.75 Å2
2--2.05 Å20 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.05→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 188 869 6025
Biso mean--22.46 30.4 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135521
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175169
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6397492
X-RAY DIFFRACTIONr_angle_other_deg1.5231.56911977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18922.311264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86915884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9671534
X-RAY DIFFRACTIONr_chiral_restr0.080.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026352
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021125
X-RAY DIFFRACTIONr_rigid_bond_restr1.255310690
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 1102 -
Rwork0.27 20922 -
all-22024 -
obs--89.83 %

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