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- PDB-7jhw: The internal aldimine crystal structure of Salmonella typhimurium... -

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Entry
Database: PDB / ID: 7jhw
TitleThe internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site and Cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / LYASE / inhibitor complex / tryptophan synthase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / 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-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: 1.65 Å
AuthorsHilario, E. / Mueller, L.J. / Dunn, M.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM097569 United States
CitationJournal: To be Published
Title: The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl ...Title: The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site and Cesium ion at the metal coordination site.
Authors: Hilario, E. / Mueller, L.J. / Dunn, M.F.
History
DepositionJul 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)74,49538
Polymers71,6022
Non-polymers2,89336
Water16,340907
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)148,98976
Polymers143,2034
Non-polymers5,78672
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area22870 Å2
ΔGint-287 kcal/mol
Surface area43790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.359, 58.400, 67.150
Angle α, β, γ (deg.)90.000, 94.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-890-

HOH

21B-908-

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 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: 42902.879 Da / Num. of mol.: 1 / Mutation: S377A
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 / Details (production host): beta-S377A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 943 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.: 20 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CS / CESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Description: Large plate-like crystal (0.20 x 0.25 x 0.35mm)
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Bicine-CsOH, 8% PEG 8,000, 4 mM Spermine, pH 8.0
PH range: 7.6-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cobra System / 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: Feb 16, 2020 / Details: Osmic Varimax HF ArcSec
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→90.423 Å / Num. obs: 71493 / % possible obs: 84.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.07 / Rrim(I) all: 0.14 / Rsym value: 0.106 / Net I/av σ(I): 4.2 / Net I/σ(I): 6.6
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
1.65-1.7440.4041.73882797700.2770.5610.4042.679.8
1.74-1.8440.2792.43601091080.1890.3830.2793.778.7
1.84-1.973.90.2023.33322884780.1340.2690.2024.977.6
1.97-2.133.80.1414.52986477790.0940.1880.1416.276.7
2.13-2.333.70.1145.52762375590.0770.1520.1147.380.5
2.33-2.613.50.1055.82730177940.0740.1420.1057.892.4
2.61-3.013.80.124.72732772120.0790.1570.128.996.8
3.01-3.6940.1085.32473262130.0660.1360.10810.397.8
3.69-5.2240.0688.41939448560.0460.0930.06810.998.4
5.22-36.4133.90.0677.11052427240.0470.0940.06710.398.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.359
Highest resolutionLowest resolution
Rotation36.42 Å1.84 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 71485
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.94-10034.70.892550
6.32-8.9440.50.885993
5.16-6.32400.8651270
4.47-5.1630.10.9051477
4-4.4728.40.9161693
3.65-4310.9261814
3.38-3.6527.30.9272015
3.16-3.3828.50.9042150
2.98-3.1627.80.9112238
2.83-2.9830.50.8892403
2.7-2.83270.9062478
2.58-2.725.60.9192599
2.48-2.5825.90.9132654
2.39-2.4827.50.9032656
2.31-2.3925.10.9052656
2.24-2.3125.10.9052580
2.17-2.2423.50.9012514
2.11-2.1723.90.9042569
2.05-2.1123.70.9152599
2-2.0523.40.9082665
1.95-223.10.9112778
1.91-1.9524.70.8932811
1.86-1.9123.80.9092932
1.83-1.8624.10.9092974
1.79-1.8323.40.9053064
1.75-1.7925.10.8943154
1.72-1.7526.80.8933239
1.69-1.7228.40.8743288
1.65-1.6934.40.8474672

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.6.04phasing
DM7.1.002phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C73

6c73


Resolution: 1.65→36.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.097 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 3523 4.9 %RANDOM
Rwork0.1758 ---
obs0.1779 67962 84.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.82 Å2 / Biso mean: 19.235 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.65→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 137 933 6078
Biso mean--32.51 32.27 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125337
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.637229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67222.278259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3615871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1391534
X-RAY DIFFRACTIONr_chiral_restr0.0960.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024093
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 215 -
Rwork0.307 4729 -
all-4944 -
obs--80.06 %

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