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- PDB-7ku9: The internal aldimine form of the wild-type Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7ku9
TitleThe internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site and another F6F molecule at the enzyme beta-site at 1.40 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 / cytosol
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-F6F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site ...Title: The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site and another F6F molecule at the enzyme beta-site at 1.40 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionNov 24, 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

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)75,79446
Polymers71,6182
Non-polymers4,17644
Water15,925884
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 area11790 Å2
ΔGint28 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.259, 58.900, 67.230
Angle α, β, γ (deg.)90.000, 94.820, 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 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 928 molecules

#3: Chemical ChemComp-F6F / 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE, F6


Mass: 329.166 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11F3NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
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: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→91.306 Å / Num. all: 136186 / Num. obs: 136186 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.041 / Rrim(I) all: 0.081 / Rsym value: 0.061 / Net I/av σ(I): 6.8 / Net I/σ(I): 8.8 / Num. measured all: 518759
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.7 / Num. measured all: 18440 / Num. unique obs: 4587 / Rpim(I) all: 0.021 / Rrim(I) all: 0.042 / Rsym value: 0.438 / Net I/σ(I) obs: 18.3 / % possible all: 82.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.473
Highest resolutionLowest resolution
Rotation36.77 Å1.63 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 136185
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.59-10037.30.906916
5.37-7.59400.8951670
4.38-5.3728.30.932122
3.79-4.38260.9282531
3.39-3.7924.50.9392824
3.1-3.3924.90.9263103
2.87-3.125.30.933420
2.68-2.8724.20.9323614
2.53-2.6824.10.9333887
2.4-2.5322.70.9364074
2.29-2.421.30.9414294
2.19-2.2921.30.9444473
2.1-2.1919.70.9484702
2.03-2.120.10.9454843
1.96-2.0320.10.9445044
1.9-1.9620.40.9395171
1.84-1.920.30.945382
1.79-1.8420.60.9425455
1.74-1.7920.50.9425691
1.7-1.7420.80.9395805
1.66-1.722.20.9395916
1.62-1.6623.70.9286095
1.58-1.62240.936216
1.55-1.5824.50.9286280
1.52-1.5526.90.9146491
1.49-1.5228.60.9086574
1.46-1.4931.30.96381
1.43-1.4633.40.8965834
1.4-1.4340.60.8387377

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.4→36.79 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1829 / WRfactor Rwork: 0.1401 / FOM work R set: 0.8403 / SU B: 2.462 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0576 / SU Rfree: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.177 6868 5 %RANDOM
Rwork0.136 ---
obs0.138 129318 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.21 Å2 / Biso mean: 20.67 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.07 Å2
2---0.73 Å20 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 1.4→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 239 892 6061
Biso mean--37.54 38.16 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125479
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6347407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69722.285267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29515887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1681534
X-RAY DIFFRACTIONr_chiral_restr0.0990.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024185
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.40135479
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 405 -
Rwork0.251 7429 -
all-7834 -
obs--76.18 %
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)
10.0235-0.0090.00130.0250.00370.0011-0.0007-0.00080.00280.00030.00110.00330.0001-0.0004-0.00050.032100.00010.0392-00.0138.03339.90528.8205
20.0669-0.054-0.00830.2746-0.00260.1873-0.0029-0.0091-0.00990.012200.00290.0021-0.00160.00280.0289-0.00020.00060.03990.00090.010546.5304-4.155918.4133
30.0257-0.0533-0.01680.18030.09850.0696-0.00250.00010.00110.0060.0036-0.0050.00310.0015-0.00110.0307-0.00060.00030.0390.00080.01152.50653.260723.1625
40.1541-0.10030.00910.12930.01560.0155-0.00510.00060.00970.00660.0017-0.0071-0.0003-0.00090.00340.0319-0.00060.00010.040.00070.009245.434924.495721.3457
50.04080.021-0.00140.0403-0.00720.0073-0.0017-0.0009-0.00880.0017-0.0002-0.0114-0.0005-0.00080.00190.03250.00040.00030.0393-0.00050.003512.3286-14.212524.7885
60.0862-0.0083-0.02030.05090.02150.03270.0023-0.00170.01660.0008-0.0006-0.007-0.0049-0.0005-0.00170.032600.00020.038-0.00030.008518.09581.549830.819
70.1363-0.002-0.00380.0337-0.00860.0023-0.00140.00120.0098-0.00040.0014-0.00120.0001-0.0001-00.0329-00.00040.0386-0.00060.00085.3392-6.715113.2386
80.06890.03610.04740.03870.0250.0638-0.00420.0010.01880.005-0.00670.01170.00260.00030.01090.0322-0.00040.00030.0412-0.00010.0055-6.6674-1.518517.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 192
3X-RAY DIFFRACTION3A193 - 234
4X-RAY DIFFRACTION4A235 - 268
5X-RAY DIFFRACTION5B2 - 100
6X-RAY DIFFRACTION6B101 - 196
7X-RAY DIFFRACTION7B197 - 364
8X-RAY DIFFRACTION8B365 - 394

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