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- PDB-4ht3: The crystal structure of Salmonella typhimurium Tryptophan Syntha... -

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Basic information

Entry
Database: PDB / ID: 4ht3
TitleThe crystal structure of Salmonella typhimurium Tryptophan Synthase at 1.30A complexed with N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE (F9) inhibitor in the alpha site, internal aldimine
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Lyase / carbon-oxygen lyase / tryptophan biosynthesis / Salmonella / F9F / Allosteric enzyme / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Pyridoxal phosphate / Cesium ion / 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 / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsHilario, E. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
CitationJournal: Biochemistry / Year: 2013
Title: Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states.
Authors: Niks, D. / Hilario, E. / Dierkers, A. / Ngo, H. / Borchardt, D. / Neubauer, T.J. / Fan, L. / Mueller, L.J. / Dunn, M.F.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 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)74,99134
Polymers71,6182
Non-polymers3,37432
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)149,98368
Polymers143,2354
Non-polymers6,74764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8500 Å2
ΔGint-32 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.850, 59.140, 67.300
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-946-

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
Details: Yang et al (1996) Protein Expression and Purification, 8:126-136.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1727, trpA / 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
Details: Yang et al (1996) Protein Expression and Purification, 8:126-136.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1726, trpB / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 10 types, 797 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-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#10: 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
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2012
RadiationMonochromator: SIBYLS KOHZU DUAL DOUBLE SI(111) CRYSTAL MONOCHROMATOR (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.299→90.614 Å / Num. all: 171588 / Num. obs: 171588 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.066 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.373.40.4891.482234244480.48996.4
1.37-1.453.40.351277914232390.35196.9
1.45-1.553.30.235373863220990.23597.8
1.55-1.683.40.1614.469603207620.16198.6
1.68-1.843.40.1086.664868192210.10899.2
1.84-2.063.40.0759.159456174150.07599.5
2.06-2.373.40.0641052826154810.06499.9
2.37-2.913.30.05710.943004131260.057100
2.91-4.113.80.0414.638708102220.04100
4.11-19.5883.60.03814.82031655750.03897.9

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Phasing

PhasingMethod: molecular replacement
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 165863
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.85-10046.40.825526
4.91-6.8544.20.8591622
4.03-4.9138.20.9011855
3.5-4.0332.90.9122620
3.14-3.526.70.9123342
2.86-3.14240.9113892
2.65-2.8623.50.9114220
2.48-2.6522.30.9224517
2.34-2.4821.80.9334812
2.22-2.3421.10.9375069
2.12-2.2220.90.9385317
2.03-2.12220.9355558
1.95-2.0322.90.9385743
1.88-1.95240.9366018
1.82-1.8825.80.9336152
1.76-1.8226.60.9336391
1.71-1.7627.30.9436558
1.66-1.7128.40.9416700
1.62-1.6629.90.9396890
1.57-1.6229.70.9397036
1.54-1.5731.40.9357096
1.5-1.5432.20.9377305
1.47-1.5320.9377413
1.44-1.4733.50.9337539
1.41-1.4434.30.9347583
1.38-1.4134.50.9267730
1.36-1.3834.80.9267836
1.33-1.3635.90.9127915
1.3-1.3344.40.90210608

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
DM6.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TJP

1tjp


Resolution: 1.3→18.36 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.1331 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.9147 / SU B: 1.315 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0438 / SU Rfree: 0.0454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1694 8300 5 %RANDOM
Rwork0.1309 ---
all0.13284 176870 --
obs0.1328 165862 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.4 Å2 / Biso mean: 17.7169 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.03 Å2
2--0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→18.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 187 765 5948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025608
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9977612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12224.108241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42215946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.431538
X-RAY DIFFRACTIONr_chiral_restr0.1240.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214250
X-RAY DIFFRACTIONr_rigid_bond_restr2.63735607
X-RAY DIFFRACTIONr_sphericity_free37.8775189
X-RAY DIFFRACTIONr_sphericity_bonded14.01156070
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 590 -
Rwork0.177 10879 -
all-11469 -
obs--91.83 %
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)
10.2228-0.0450.12290.01740.01030.2156-0.00150.00810.0001-0.00040.00080.0001-0.00440.01440.00070.0068-0.0006-0.0020.00180.00030.005660.052638.2-24.7556
20.00220.0018-0.00210.00540.00020.00420.0002-0.000100-0.00010.0002-0.00020-0.00010.00650-0.00190.00240.00010.005641.26240.0458-23.9265
30.0094-0.0111-0.01320.03150.01580.0371-0.00010-0.00020.0012-0.00020.00050.001800.00030.0062-0.0002-0.00210.00210.00020.005746.680328.2133-14.1337
40.32-0.326-0.26870.5110.45970.4479-0.0242-0.01840.00890.04480.0231-0.01080.0510.01880.00110.0130.0005-0.00150.0014-0.00010.006754.948927.0682-7.9845
50.0071-0.0030.00160.01170.00130.0054-0.0003-0.00130.00030.00050.00060-0.00040.0006-0.00030.0065-0.0001-0.00180.002300.005550.542145.6661-11.2263
60.00970.007-0.0050.0066-0.00450.0075-0.0001-0.0004-0.000100-0.00040.00030.00080.00010.00660.0001-0.00190.002100.005730.430516.4238-14.0972
70.0309-0.00950.01790.0031-0.00640.0180.0007-0.001-0.0008-0.0003-0.00030.00030.0011-0.0005-0.00040.0066-0.0001-0.00190.002100.00583.973911.759-5.8138
80.00860.00170.00970.00240.00440.0139-0.001-0.0010.00080.00010.00010.0002-0.0007-0.00080.00090.00660-0.00190.00210.00010.00588.726917.5047-5.8458
90.0087-0.01830.01290.0406-0.03020.02560.00110.0002-0.00120.000800.0017-0.0014-0.0001-0.00110.0067-0.0002-0.00190.0022-0.00010.005619.029125.48320.1627
100.0120.00450.00740.0121-0.01310.0290.00050.00040.00060.00210.00060.001-0.0018-0.001-0.0010.00680.0001-0.00180.0022-0.00010.006116.967936.6305-1.357
110.00640.0027-0.00080.00130.00010.001-0.0001-0.00020.0001-0.0001-0.00010-0.00020.00030.00020.00660-0.00190.00240.00010.005815.502218.1811-12.3527
120.00550-0.00060.0016-0.00190.00220.00010.00030.0006-0.0001-0.0002-0.000300.00020.00010.00670.0001-0.00190.00240.00010.005714.554629.5521-24.5201
130.0145-0.0072-0.00970.00610.00220.0140.00060.0015-0.0001-0.0001-0.0005-0.0001-0.0005-0.0006-0.00010.0064-0.0001-0.0020.00200.00575.142925.1942-20.9973
140.00240.00570.00810.01540.01430.0392-0.000600.0001-0.00090.00010.0008-0.0037-0.00160.00050.00650.0003-0.00180.00240.00010.0059-3.794426.7142-17.0277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 159
3X-RAY DIFFRACTION3A160 - 187
4X-RAY DIFFRACTION4A188 - 202
5X-RAY DIFFRACTION5A203 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 70
8X-RAY DIFFRACTION8B71 - 100
9X-RAY DIFFRACTION9B101 - 126
10X-RAY DIFFRACTION10B127 - 165
11X-RAY DIFFRACTION11B166 - 244
12X-RAY DIFFRACTION12B245 - 301
13X-RAY DIFFRACTION13B302 - 343
14X-RAY DIFFRACTION14B344 - 394

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