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- PDB-4xug: Crystal structure of Tryptophan Synthase from Salmonella typhimur... -

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Entry
Database: PDB / ID: 4xug
TitleCrystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with 2-({[4-(Trifluoromethoxy)Phenyl]Sulfonyl}Amino)Ethyl Dihydrogen Phosphate (F9F) inhibitor in the alpha site and ammonium ion in the metal coordination site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / carbon-oxygen lyase / hydro-lyase / tryptophan biosynthesis / Salmonella typhimurium / F9F / inhibitor / allosteric enzyme / aromatic amino acid biosynthesis / pyridoxal phosphate / 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. / Rossmann fold - #1100 / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F9F / AMMONIUM ION / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsHilario, E. / Caulkins, B.G. / Young, R.P. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097569 United States
CitationJournal: To Be Published
Title: Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with 2-({[4-(Trifluoromethoxy)Phenyl]Sulfonyl}Amino)Ethyl Dihydrogen Phosphate (F9F) inhibitor in the alpha site ...Title: Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with 2-({[4-(Trifluoromethoxy)Phenyl]Sulfonyl}Amino)Ethyl Dihydrogen Phosphate (F9F) inhibitor in the alpha site and ammonium ion in the metal coordination site.
Authors: Hilario, E. / Caulkins, B.G. / Young, R.P. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJan 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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)72,3106
Polymers71,6182
Non-polymers6924
Water13,439746
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)144,62012
Polymers143,2354
Non-polymers1,3858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8810 Å2
ΔGint-29 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.883, 58.860, 67.303
Angle α, β, γ (deg.)90.000, 94.670, 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
Details: Tryptophan Synthase chain A
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA / Plasmid: Derivative of Pbr322 / 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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB / Plasmid: Derivative of Pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 5 types, 750 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
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Bicine-NH4OH, 7-12% PEG 8,000, 2 mM Spermine, pH 7.8, 100mM NH4Cl
PH range: 7.6-7.9

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2012
RadiationMonochromator: VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→29.43 Å / Num. all: 84215 / Num. obs: 84215 / % possible obs: 98.7 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Rsym value: 0.08 / Net I/σ(I): 11.7 / Num. measured all: 529960
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
1.65-1.7460.3353.372162119860.9490.0170.03997
5.22-29.417.20.03926.11997127920.9980.0210.05199.3

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Phasing

PhasingMethod: molecular replacement
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.94-10020.90.931561
6.32-8.9422.90.9441019
5.16-6.3224.80.9291308
4.47-5.1616.20.9621524
4-4.4714.70.9591743
3.65-415.80.9551907
3.38-3.6514.40.9542079
3.16-3.3815.50.9522223
2.98-3.1615.70.9462336
2.83-2.9817.50.9332489
2.7-2.8317.40.942591
2.58-2.715.80.9462721
2.48-2.5817.50.9382857
2.39-2.4817.20.9372938
2.31-2.3916.40.9423046
2.24-2.3116.30.9493116
2.17-2.2416.60.953231
2.11-2.1716.60.9443345
2.05-2.1116.90.9433406
2-2.0518.50.9343513
1.95-2190.933548
1.91-1.9519.40.9393634
1.86-1.91200.9273715
1.83-1.8621.50.9263802
1.79-1.8322.30.9293845
1.75-1.7924.70.9273964
1.72-1.7525.50.9233991
1.69-1.72250.9184027
1.65-1.6933.50.8715668

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.65→29.43 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1648 / FOM work R set: 0.8607 / SU B: 3.627 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0902 / SU Rfree: 0.0888 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 4194 5 %RANDOM
Rwork0.1648 79953 --
obs0.1663 84147 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.23 Å2 / Biso mean: 22.31 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.65→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 42 760 5796
Biso mean--19.88 34.58 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195268
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9767144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50623.894226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99115876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2921536
X-RAY DIFFRACTIONr_chiral_restr0.1250.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214028
X-RAY DIFFRACTIONr_mcbond_it0.9461.5012707
X-RAY DIFFRACTIONr_mcangle_it1.5262.2433403
X-RAY DIFFRACTIONr_scbond_it1.5771.7182560
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 296 -
Rwork0.262 5681 -
all-5977 -
obs--95.51 %
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)
11.63350.7843-0.25660.7180.14770.4320.14360.13450.01050.0268-0.0740.0241-0.1395-0.1598-0.06960.05720.04290.03580.07150.00770.0501-54.33291.344321.51
20.337-0.10790.02870.6031-0.04550.32670.0432-0.01670.00780.0201-0.0359-0.016-0.03810.0029-0.00730.0280.00390.02190.0301-0.00250.0377-40.5174-0.913724.6043
30.75150.3325-0.19290.5878-0.17030.9220.04440.1269-0.0417-0.01030.0120.00390.0457-0.13-0.05640.00930.0074-0.01360.0464-0.01660.0426-46.7925-12.242814.2386
43.97933.866-3.8864.9093-5.6347.0456-0.02970.5387-0.0391-0.27340.35720.25690.3348-0.4074-0.32740.08390.0825-0.10150.1804-0.11120.1243-55.1608-13.2398.1
50.38090.01520.23980.50090.14690.47050.02170.07360.0306-0.1166-0.00870.0299-0.0784-0.0746-0.0130.04170.03160.00070.06370.02380.0327-50.38335.40211.1626
60.3306-0.05610.01370.01680.04690.3322-0.01370.0488-0.04490.0021-0.00980.0114-0.0018-0.00390.02350.00180.00150.00660.0401-0.01020.0378-15.0753-25.09618.8224
70.0130.02840.0170.73740.24250.81840.02620.00570.0093-0.05710.0167-0.0636-0.0916-0.0564-0.0430.0620.0140.03360.062-0.0130.0262-17.6449-7.8250.7317
80.2359-0.0463-0.06310.0123-0.00140.14330.00590.00360.0181-0.0041-0.008-0.00540.0186-0.02590.00210.0043-0.00210.00730.0585-0.00410.0421-15.0883-17.567217.3322
90.42480.2529-0.15580.1513-0.09060.4170.0012-0.0340.00160.0008-0.01420.001-0.01890.00790.0130.00470.00150.01070.0531-0.00320.0365-5.1627-15.156220.9619
100.0964-0.15920.02520.2729-0.1451.14230.0208-0.0323-0.0063-0.01840.05190.0168-0.14090.0992-0.07270.0247-0.01660.01240.0869-0.00520.0164.0483-13.600917.142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 187
4X-RAY DIFFRACTION4A188 - 202
5X-RAY DIFFRACTION5A203 - 267
6X-RAY DIFFRACTION6B2 - 100
7X-RAY DIFFRACTION7B101 - 165
8X-RAY DIFFRACTION8B166 - 301
9X-RAY DIFFRACTION9B302 - 343
10X-RAY DIFFRACTION10B344 - 395

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