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

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Basic information

Entry
Database: PDB / ID: 7lpf
TitleThe internal aldimine 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 sodium ion at the metal coordination site at 1.10 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / inhibitor / internal aldimine / LYASE / LYASE-LYASE INHIBITOR 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-F9F / 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: 1.1 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 in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the ...Title: The internal aldimine 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 sodium ion at the metal coordination site at 1.10 Angstrom resolution
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: 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)72,5779
Polymers71,6182
Non-polymers9607
Water13,781765
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)145,15518
Polymers143,2354
Non-polymers1,92014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13200 Å2
ΔGint-40 kcal/mol
Surface area43400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.233, 59.182, 67.325
Angle α, β, γ (deg.)90.000, 94.700, 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 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 772 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 765 / 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: 51.31 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-NaOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
PH range: 7.6-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.099→90.81 Å / Num. obs: 278268 / % possible obs: 96.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.06 / Rrim(I) all: 0.12 / Rsym value: 0.091 / Net I/av σ(I): 4.1 / Net I/σ(I): 3.2
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
1.1-1.163.40.7030.7128798382000.5211.0010.7031.190.8
1.16-1.233.80.4451.1151209397730.310.6130.4451.9100
1.23-1.313.90.3441.3145103374200.2420.4810.3442.2100
1.31-1.423.90.2092.2136282347700.1430.2880.2092.8100
1.42-1.563.90.1642.2126183320910.1140.2270.1643.6100
1.56-1.7440.0776.4115328290870.0480.0980.0774.3100
1.74-2.013.90.0785.3100838255930.050.1010.078599.9
2.01-2.463.80.0616.483152217130.040.080.0615.399.8
2.46-3.483.90.04513.360497156960.0270.0550.0455.593.1
3.48-28.4993.10.0718.21223839250.0420.0810.0714.941.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.766
Highest resolutionLowest resolution
Rotation28.5 Å1.24 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 278092
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.96-100620.711555
4.22-5.96520.8411344
3.44-4.2248.90.8912206
2.98-3.44360.94230
2.67-2.9826.10.9155691
2.43-2.6724.10.9226430
2.25-2.4322.70.9256910
2.11-2.2521.80.9327484
1.99-2.11240.9197915
1.89-1.9926.60.9078425
1.8-1.8929.70.8978778
1.72-1.832.90.8859246
1.65-1.7235.90.8819588
1.59-1.65380.87610002
1.54-1.5940.40.86610371
1.49-1.5443.50.82610700
1.45-1.4945.90.82810941
1.41-1.4549.20.81411406
1.37-1.41510.77711652
1.33-1.3753.70.73512025
1.3-1.3354.20.73112282
1.27-1.356.90.71112566
1.24-1.2758.10.69312824
1.22-1.2460.50.68413181
1.19-1.2262.20.68913406
1.17-1.1965.50.65913627
1.15-1.1773.10.57913962
1.13-1.1578.10.56214030
1.1-1.1378.30.57516315

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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: 1.1→28.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.763 / SU ML: 0.036 / SU R Cruickshank DPI: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 13730 4.9 %RANDOM
Rwork0.172 ---
obs0.1733 264362 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 227.64 Å2 / Biso mean: 16.851 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.08 Å2
2---0.78 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 1.1→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 0 57 781 5805
Biso mean--21.64 33.96 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135371
X-RAY DIFFRACTIONr_bond_other_d0.0080.0174960
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6397308
X-RAY DIFFRACTIONr_angle_other_deg1.5581.57111514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40222.105266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2515872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831536
X-RAY DIFFRACTIONr_chiral_restr0.0810.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026241
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021114
X-RAY DIFFRACTIONr_rigid_bond_restr4.41335370
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 868 -
Rwork0.343 16564 -
all-17432 -
obs--82.21 %

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