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

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Basic information

Entry
Database: PDB / ID: 7kwv
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 and cesium ion at the metal coordination site at 1.30 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 / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / 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: 1.3 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 and cesium ion at the metal coordination site at 1.30 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 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)73,50616
Polymers71,6182
Non-polymers1,88914
Water14,574809
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)147,01332
Polymers143,2354
Non-polymers3,77728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14470 Å2
ΔGint-192 kcal/mol
Surface area43140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.189, 59.730, 67.540
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-740-

HOH

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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 / 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, 823 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.6 Å3/Da / Density % sol: 52.75 % / 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: 7.8-8.0 / 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: Mar 16, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→91.794 Å / Num. obs: 159927 / % possible obs: 89.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.047 / Rrim(I) all: 0.087 / Rsym value: 0.063 / Net I/av σ(I): 7.7 / Net I/σ(I): 5.8
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
1.3-1.373.20.541.369264215760.3990.7510.541.482.9
1.37-1.453.10.391.764500205040.2880.540.391.983
1.45-1.5530.2622.160007197750.1980.3680.2622.685.2
1.55-1.682.90.1614.656051191320.1160.2130.1613.588.6
1.68-1.842.80.1086.451796182700.0780.1410.1084.891.7
1.84-2.062.80.0826.447781169930.0610.110.0827.194.3
2.06-2.372.80.0658.242426152960.0510.090.0659.796.2
2.37-2.912.80.04912.637346132550.0380.0670.04911.298.1
2.91-4.113.60.03915.836784103080.0270.0520.03915.998.5
4.11-28.7433.30.03417.81575648180.0250.0460.03415.482.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.661
Highest resolutionLowest resolution
Rotation28.75 Å1.6 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 159121
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.05-10052.30.833644
4.98-7.0542.40.8921931
4.07-4.9831.10.9162413
3.52-4.0725.30.933087
3.15-3.5224.60.9263572
2.88-3.1522.90.923995
2.66-2.88230.9174277
2.49-2.6623.40.9174449
2.35-2.4922.60.9144838
2.23-2.3521.30.9165014
2.12-2.2321.10.9265249
2.03-2.12210.9245458
1.95-2.03230.8955632
1.88-1.9523.70.8655738
1.82-1.8824.20.895906
1.76-1.8225.30.8896035
1.71-1.76260.8716188
1.66-1.7127.90.8716353
1.62-1.6629.70.8736375
1.58-1.6230.30.8496571
1.54-1.5832.80.8246553
1.5-1.5433.60.8066692
1.47-1.534.30.8216713
1.44-1.4737.30.8036808
1.41-1.4439.90.8016908
1.38-1.4143.10.7766992
1.36-1.3843.70.7447167
1.33-1.3649.30.7597319
1.3-1.3356.20.70310244

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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: 4JT3

4jt3


Resolution: 1.3→28.76 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.648 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0555 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.199 7876 4.9 %RANDOM
Rwork0.1575 ---
obs0.1596 151245 88.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.13 Å2 / Biso mean: 21.974 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20.16 Å2
2---0.14 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.3→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5003 0 108 828 5939
Biso mean--30.35 40.05 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125518
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6367501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63522275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47715912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8411538
X-RAY DIFFRACTIONr_chiral_restr0.10.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024325
X-RAY DIFFRACTIONr_rigid_bond_restr2.07735517
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 574 -
Rwork0.3 10318 -
all-10892 -
obs--82.86 %
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)
10.00490.0098-0.00240.0226-0.0020.004-0.0002-0.0006-0.00090.0016-0.0001-0.00360.00050.0020.00030.00320.0001-0.00470.01130.00030.0073-40.2114-19.739925.357
20.03890.0373-0.00520.0629-0.02160.015-0.0030.00270.0028-0.00510.00490.00260.0041-0.0018-0.00190.0035-0.0005-0.00420.01130.00040.006-48.7232-29.950811.253
30.0160.01550.0070.04660.00070.0044-0.0014-0.00060.003-0.0020.00050.0032-0.00030.00070.00090.0028-0.0007-0.0040.0114-00.0059-48.8768-12.210911.5945
40.00170.00090.00030.0020.00010.0006-0.00010.00020.0001-0.00010.00010.000200.0001-0.00010.0026-0-0.00430.010900.007-12.9757-36.705212.9294
50.0162-0.01270.0320.0548-0.04860.0777-0.00250.00270.00260.0014-0.0035-0.0036-0.00480.00150.00610.00230.0001-0.0040.0099-00.00724.2522-31.012215.5081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 202
3X-RAY DIFFRACTION3A203 - 268
4X-RAY DIFFRACTION4B2 - 364
5X-RAY DIFFRACTION5B365 - 396

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