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- PDB-7lt4: The aminoacrylate form of the beta-K167T mutant Tryptophan Syntha... -

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Basic information

Entry
Database: PDB / ID: 7lt4
TitleThe aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / inhibitor / aminoacrylate form / tryptophan synthase
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-0JO / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the ...Title: The aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 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)74,13531
Polymers71,5902
Non-polymers2,54529
Water8,071448
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)148,27062
Polymers143,1794
Non-polymers5,09158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18270 Å2
ΔGint-253 kcal/mol
Surface area41800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.419, 59.426, 67.332
Angle α, β, γ (deg.)90.000, 94.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-421-

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: 42890.805 Da / Num. of mol.: 1 / Mutation: K167T
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, STM1726 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 477 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, 8% PEG 8,000, 4 mM Spermine, pH 7.6
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: Oct 6, 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: 1.796→91.394 Å / Num. obs: 65313 / % possible obs: 97 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.068 / Rrim(I) all: 0.123 / Rsym value: 0.087 / Net I/av σ(I): 5.3 / Net I/σ(I): 6.3
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
1.8-1.93.30.31123027192490.2290.4150.3113.295
1.9-2.013.30.2332.62905588640.1710.310.2334.295.6
2.01-2.153.30.1823.32746583860.1360.2450.1824.996.3
2.15-2.323.30.1493.42559378290.1140.2060.1495.596.7
2.32-2.553.30.1234.72377773030.0940.1690.1236.397.7
2.55-2.853.30.162161366440.0780.1410.17.498
2.85-3.293.30.0847.11921058990.0650.1190.0848.898.7
3.29-4.023.30.0616.71647850300.0480.0870.0611099
4.02-5.693.30.0414.31268839030.0350.0630.0410.298.6
5.69-29.7133.20.03513.4704122060.0340.0620.03510.198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.433
Highest resolutionLowest resolution
Rotation29.71 Å1.91 Å

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Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KWV

7kwv


Resolution: 1.8→29.71 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 3379 5.2 %
Rwork0.1984 61554 -
obs0.2007 64933 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.76 Å2 / Biso mean: 26.9219 Å2 / Biso min: 3.33 Å2
Refinement stepCycle: final / Resolution: 1.8→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 122 479 5511
Biso mean--36.14 33 -
Num. residues----661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.30961240.24782479260394
1.83-1.850.261260.24772521264795
1.85-1.880.29221680.24872430259895
1.88-1.910.25161210.23432543266495
1.91-1.950.26281290.22462507263695
1.95-1.980.26421170.21622540265795
1.98-2.020.24611470.21782502264996
2.02-2.060.25651450.21362530267596
2.06-2.10.27161430.21492512265595
2.11-2.150.24211480.21982507265597
2.15-2.210.26821490.21642585273497
2.21-2.270.28091460.21482527267396
2.27-2.330.22091470.20592519266696
2.33-2.410.30671390.21912609274897
2.41-2.50.28051310.21862586271797
2.5-2.60.26981490.20892560270997
2.6-2.710.23341360.19892607274398
2.71-2.860.23671640.1972556272098
2.86-3.040.23381390.19242634277398
3.04-3.270.24641550.18562603275898
3.27-3.60.21811480.17162639278799
3.6-4.120.24271440.16912624276898
4.12-5.180.17661410.15932658279998
5.18-29.710.20941230.1972776289999
Refinement TLS params.Method: refined / Origin x: -24.084 Å / Origin y: -16.2389 Å / Origin z: 15.9466 Å
111213212223313233
T0.1216 Å20.051 Å20.0006 Å2-0.0912 Å2-0.0004 Å2--0.1045 Å2
L0.8902 °2-0.1153 °2-0.5876 °2-0.3239 °20.3698 °2--0.8076 °2
S0.1774 Å °0.1362 Å °0.1508 Å °-0.109 Å °-0.1464 Å °0.0953 Å °-0.1963 Å °-0.2537 Å °0.0228 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 268
2X-RAY DIFFRACTION1allA302 - 701
3X-RAY DIFFRACTION1allB2 - 1101
4X-RAY DIFFRACTION1allC2 - 8
5X-RAY DIFFRACTION1allD1 - 3
6X-RAY DIFFRACTION1allE1 - 52

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