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- PDB-6xt0: Salmonella typhimurium tryptophan synthase complexed with dioxind... -

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Basic information

Entry
Database: PDB / ID: 6xt0
TitleSalmonella typhimurium tryptophan synthase complexed with dioxindolyl-L-alanine and D-glycerol-3-phosphate
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / multi-enzyme complex / allosteric enzyme product 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 / 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
SN-GLYCEROL-1-PHOSPHATE / Chem-VE4 / Chem-X9D / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPhillips, R.S.
CitationJournal: Biochemistry / Year: 2021
Title: Structural Basis of the Stereochemistry of Inhibition of Tryptophan Synthase by Tryptophan and Derivatives.
Authors: Phillips, R.S. / Harris, A.P.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 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)73,91521
Polymers71,6182
Non-polymers2,29819
Water15,781876
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)147,83142
Polymers143,2354
Non-polymers4,59638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area15500 Å2
ΔGint-34 kcal/mol
Surface area43790 Å2
Unit cell
Length a, b, c (Å)184.790, 59.190, 67.350
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-563-

HOH

21B-804-

HOH

31B-881-

HOH

41B-994-

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 (bacteria) / Gene: trpA, DD95_04145 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6FWC1, UniProt: P00929*PLUS, 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) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 895 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Chemical ChemComp-X9D / 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate


Mass: 465.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O9P
#6: Chemical ChemComp-VE4 / 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate


Mass: 465.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O9P
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.05 M bicine, pH 7.8, 5 mM EDTA, 0.1 mM PLP, 1 mM DTT, and 1 mM spermine tetrahydrochloride with 6-8% glycerol and 10-12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.321→92.044 Å / Num. obs: 86081 / % possible obs: 87.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.06 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.6
Reflection shellResolution: 1.32→1.48 Å / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.1 / % possible all: 75.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TYS

2tys


Resolution: 1.37→46.02 Å / SU ML: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.843
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.198 2010 2.43 %
Rwork0.159 --
obs0.16 82559 53.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.42 Å2
Refinement stepCycle: LAST / Resolution: 1.37→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 135 883 6028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065555
X-RAY DIFFRACTIONf_angle_d0.7627567
X-RAY DIFFRACTIONf_dihedral_angle_d18.4912079
X-RAY DIFFRACTIONf_chiral_restr0.063821
X-RAY DIFFRACTIONf_plane_restr0.0051006
LS refinement shellResolution: 1.37→1.4 Å
RfactorNum. reflection% reflection
Rfree0.2221 10 -
Rwork-4303 -
obs--75 %
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)
16.04411.7303-0.31242.3061-1.19021.87170.11160.15130.1309-0.1613-0.08010.53670.0054-0.4487-0.07630.13920.06890.00120.2807-0.12570.380838.12230.50920.5775
24.2781-0.806-1.08121.145-0.06292.21180.04320.02450.2947-0.0585-0.07420.0924-0.2604-0.02890.04340.14090.01430.01350.1247-0.0350.236253.413535.84423.4106
33.9375-3.3792-1.34943.85640.85031.36480.0385-0.15830.17050.1168-0.09430.1667-0.0561-0.13310.05330.0806-0.02130.03280.1255-0.02170.144451.962922.73428.1718
41.6833-0.0152.27231.8201-0.78663.51240.0538-0.0283-0.2147-0.0018-0.17990.29980.1528-0.2620.13180.0944-0.00560.02570.1797-0.02190.214147.766515.020523.8243
55.58393.209-0.48774.2797-0.01912.3333-0.10740.6862-0.3374-0.47080.07260.21150.2475-0.33770.01050.180.0658-0.06190.3005-0.10850.331443.517217.196210.6505
64.73032.74270.40272.96960.41371.4227-0.03460.44580.2289-0.32750.0030.388-0.1646-0.15080.04020.17950.1092-0.04030.2647-0.05250.256643.496431.011610.2923
75.6028-0.55631.35964.84670.24235.85640.06240.26640.8241-0.3504-0.270.6271-0.4987-0.4020.19290.28430.156-0.00920.26280.0070.382941.463442.95412.9893
82.2912-0.8742-0.51351.00320.66281.97850.07180.1233-0.133-0.0556-0.11840.06710.1162-0.34150.05680.0743-0.0389-0.01620.11530.00010.111961.90044.512413.7469
92.61890.40320.65560.8760.57871.93220.08020.1754-0.13680.009-0.04830.00860.22060.1676-0.0950.05910.00270.02740.04430.01020.053190.52330.7636.8158
101.3275-0.48311.21490.5232-0.51051.84750.02780.0546-0.0379-0.0278-0.01670.0451-0.0485-0.0967-0.00950.09490.01070.00840.1263-0.01680.07279.16689.67623.307
113.4858-1.4976-2.54973.59061.86345.61780.2289-0.1620.48690.01450.1535-0.2883-0.5770.3949-0.33190.17990.01230.05490.14350.00890.133977.133625.04152.088
120.68330.0843-0.06220.19870.08710.60510.01450.00150.03660.0038-0.0260.0292-0.0058-0.02970.01220.0754-0.00340.00520.0952-0.00310.066781.010111.912318.5208
130.9542-0.44771.07541.2596-0.89762.6574-0.14660.10880.20660.0585-0.0149-0.1724-0.42220.2080.13450.1367-0.03320.01250.1664-0.00630.125196.743917.648715.6018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 29 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 30 THROUGH 91 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 92 THROUGH 136 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 137 THROUGH 159 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 160 THROUGH 202 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 203 THROUGH 247 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 248 THROUGH 268 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 2 THROUGH 37 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 38 THROUGH 70 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 71 THROUGH 126 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 127 THROUGH 165 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 166 THROUGH 364 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 365 THROUGH 397 )

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