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- PDB-6xe3: Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 6xe3
TitleSalmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / Protein complex
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-1D0 / : / Chem-F9F / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
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: Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJun 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 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

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)75,04645
Polymers71,6022
Non-polymers3,44443
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-204 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.517, 59.427, 67.063
Angle α, β, γ (deg.)90.000, 94.640, 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Details (production host): beta-S377A / 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, 785 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.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-1D0 / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid


Mass: 425.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 2.53 Å3/Da / Density % sol: 51.34 % / 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, 4 mM Spermine, pH 7.8
PH range: 7.6-8.0

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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: Apr 19, 2019 / 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: 1.55→90.461 Å / Num. all: 97942 / Num. obs: 97942 / % possible obs: 95 % / Redundancy: 3.8 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.078 / Rsym value: 0.05 / Net I/av σ(I): 6.3 / Net I/σ(I): 10.8 / Num. measured all: 375144
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
1.55-1.632.70.1634.129292108870.1540.260.1633.773
1.63-1.733.80.154452737137270.110.2170.1545.597
1.73-1.853.90.1145.851153130440.0820.1620.1147.297.9
1.85-23.90.0867.348190122080.0640.1270.0869.598.6
2-2.1940.0688.845175113650.0510.10.06811.999.1
2.19-2.4540.0619.341253103170.0470.0920.06113.799.7
2.45-2.8340.05410.73702991690.040.080.05415.499.9
2.83-3.474.10.0510.13175677730.0360.0720.0517.599.9
3.47-4.94.10.03913.22487760590.0290.0590.03919.1100
4.9-38.95340.0368.21368233930.0350.070.03618.599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.491
Highest resolutionLowest resolution
Rotation38.95 Å1.77 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 97915
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.4-10035.10.889697
5.94-8.4420.8641222
4.85-5.94360.8771582
4.2-4.8529.40.9041844
3.76-4.228.20.9052094
3.43-3.7626.50.9212309
3.18-3.4327.20.9162482
2.97-3.1826.70.912700
2.8-2.97290.8952830
2.66-2.827.90.8843038
2.53-2.6626.10.9033173
2.43-2.53250.913293
2.33-2.4325.60.9083409
2.25-2.3325.20.9093551
2.17-2.2525.20.9073676
2.1-2.1726.10.9013795
2.04-2.1250.8983875
1.98-2.0426.40.8984012
1.93-1.9825.70.894119
1.88-1.9326.70.8884230
1.83-1.8827.20.8844268
1.79-1.8327.20.8824397
1.75-1.7928.80.8724462
1.71-1.7527.50.8724617
1.68-1.7128.90.8654623
1.65-1.68300.8494709
1.62-1.6531.80.8514542
1.59-1.6232.20.8273985
1.55-1.5939.50.7894381

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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_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HPJ

4hpj


Resolution: 1.55→38.95 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.88 / SU ML: 0.063 / SU R Cruickshank DPI: 0.1115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 4983 5.1 %RANDOM
Rwork0.1739 ---
obs0.1771 92932 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.07 Å2 / Biso mean: 22.523 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.1 Å2
2--0.28 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.55→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 159 770 5946
Biso mean--33.26 36.1 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125383
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.6367284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71522.21267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5561535
X-RAY DIFFRACTIONr_chiral_restr0.0920.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024147
X-RAY DIFFRACTIONr_rigid_bond_restr2.13435382
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 223 -
Rwork0.216 4459 -
all-4682 -
obs--61.69 %

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