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- PDB-7kyt: The aminoacrylate form of the wild-type Salmonella typhimurium Tr... -

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Basic information

Entry
Database: PDB / ID: 7kyt
TitleThe aminoacrylate 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 benzimidazole (BZI) at the enzyme beta-site at 1.35 Angstrom resolution
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 / tryptophan biosynthetic process / identical protein binding / 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-0JO / BENZIMIDAZOLE / : / Chem-F9F / 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: 1.35 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 wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme ...Title: The aminoacrylate 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 benzimidazole (BZI) at the enzyme beta-site at 1.35 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 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)73,33715
Polymers71,6182
Non-polymers1,71913
Water11,764653
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 area5270 Å2
ΔGint-65 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.460, 61.250, 67.560
Angle α, β, γ (deg.)90.000, 94.570, 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: 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 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 666 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-BZI / BENZIMIDAZOLE / Benzimidazole


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.68 Å3/Da / Density % sol: 54.13 % / 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: 7.8 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-Jet crystal cryocoolers / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→91.937 Å / Num. obs: 162194 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Rsym value: 0.078 / Net I/av σ(I): 6.4 / Net I/σ(I): 5.7
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
1.35-1.423.30.8380.976845235320.61.1060.8381.198.6
1.42-1.513.30.5641.373276223390.4080.7540.5641.699
1.51-1.613.30.3751.970533211830.2710.5050.3752.499.4
1.61-1.743.40.249366712197340.1770.3330.2493.599.6
1.74-1.913.40.1644.461349181400.1180.2220.1644.999.4
1.91-2.133.40.16.855561163320.0730.1360.18.198.8
2.13-2.463.20.0738.545433144110.0560.1010.07310.198.5
2.46-3.0230.078.336889122380.0540.0980.0711.898.9
3.02-4.273.70.0413.73476495170.0290.0550.0416.198.9
4.27-19.5663.50.02424.61670847680.0190.0370.02416.289

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.492
Highest resolutionLowest resolution
Rotation19.57 Å1.57 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 162102
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.32-10043.50.867716
5.17-7.3236.20.9031847
4.22-5.1724.60.9342343
3.66-4.2221.80.9282879
3.27-3.6620.40.9263302
2.99-3.2721.20.9143661
2.77-2.9921.40.8993946
2.59-2.7721.50.9054205
2.44-2.5921.50.9054433
2.31-2.44200.9164709
2.21-2.3119.30.9274946
2.11-2.2119.10.9375145
2.03-2.1120.60.935428
1.96-2.0320.80.9175665
1.89-1.96230.9065832
1.83-1.8924.50.8895994
1.77-1.8325.40.8976268
1.72-1.7726.10.9016389
1.68-1.7227.30.96646
1.64-1.6828.70.9026828
1.6-1.64300.9026931
1.56-1.630.70.9027109
1.53-1.5633.30.8887241
1.49-1.5335.20.8947353
1.46-1.4937.80.8947595
1.44-1.4640.30.8987717
1.41-1.44440.8947771
1.38-1.4148.30.8998005
1.35-1.3852.50.85811198

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data 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: 7KXC

7kxc


Resolution: 1.35→19.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.209 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 8247 5.1 %RANDOM
Rwork0.1745 ---
obs0.1763 153855 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.69 Å2 / Biso mean: 23.314 Å2 / Biso min: 9.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å20.4 Å2
2---1.71 Å2-0 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 1.35→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 99 669 5750
Biso mean--35.73 41.24 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125401
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.6357332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11921.94268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5315888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4291537
X-RAY DIFFRACTIONr_chiral_restr0.0990.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024221
X-RAY DIFFRACTIONr_rigid_bond_restr4.36535400
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 598 -
Rwork0.334 11272 -
all-11870 -
obs--98.29 %
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)
10.0162-0.0028-0.00540.02-0.00050.0023-0.003-0.00090.0006-0.00050.0018-0.0017-0.0008-0.00170.00120.01290.0009-0.00980.0292-0.00050.00838.60218.002310.2532
21.03870.00110.237200.00010.0555-0.0078-0.11620.1125-0.0002-0.00860.00020.0027-0.01950.01640.0250.001-0.01640.0641-0.01310.022951.2369-0.534626.2787
30.02270.02170.01640.03260.01670.0122-0.0041-0.00550.0030.00230.0035-0.0072-0.0016-0.00550.00050.01310.0042-0.00790.0297-0.00080.011646.251517.53821.8587
40.0340.05690.01220.1091-0.00920.06850.0052-0.002-0.00130.0055-0.0058-0.00080.00360.00430.00050.012-0.0004-0.01020.0251-0.00140.009227.831-13.065319.7769
50.1168-0.05730.11470.0296-0.05590.12480.0088-0.012-0.0125-0.0030.00180.00430.0017-0.0058-0.01050.011-0.0022-0.00910.02630.00080.00961.3979-17.931228.1034
60.02430.01760.00210.01930.00640.0039-0.0005-0.0002-0.0021-0.00240.0016-0.0033-0.0018-0.0006-0.00110.01260-0.01010.0311-0.00010.010110.1995-8.80730.3402
70.0633-0.0216-0.00390.0304-0.03860.0696-0.0051-0.00010.00220.00140.0005-0.00350.001-0.00140.00450.01090.0003-0.01020.0287-0.00050.010111.88756.588931.2203
80.0207-0.0034-0.01080.00060.00180.0070.00210.00020.0004-0.0004-0.0007-0.0001-0.0002-0.0008-0.00150.0131-0.0002-0.01090.0321-00.009312.2839-7.216715.1476
90.2436-0.0307-0.16770.1663-0.02440.12840.01380.00650.00940.0079-0.00340.0146-0.0121-0.0017-0.01030.0140.0001-0.00970.0318-0.00020.0117-6.4322-1.462414.3926
100.02980.036-0.00930.06050.02180.0692-0.0012-0.00160.00380.0012-0.00440.00610.00090.00260.00560.01350.0007-0.01170.0320.00020.0114-6.2952-3.290116.578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 187
2X-RAY DIFFRACTION2A188 - 202
3X-RAY DIFFRACTION3A203 - 268
4X-RAY DIFFRACTION4B2 - 37
5X-RAY DIFFRACTION5B38 - 70
6X-RAY DIFFRACTION6B71 - 126
7X-RAY DIFFRACTION7B127 - 165
8X-RAY DIFFRACTION8B166 - 322
9X-RAY DIFFRACTION9B323 - 343
10X-RAY DIFFRACTION10B344 - 394

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