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- PDB-6d0v: Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-... -

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Basic information

Entry
Database: PDB / ID: 6d0v
TitleTryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / F9F ligand / cesium ion / mutant beta-Q114A / Lyase / P1T ligand / 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-0JO / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
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: Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ...Title: Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Apr 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _audit_author.identifier_ORCID / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct.title / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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.ptnr2_symmetry
Revision 2.2Oct 4, 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)74,71239
Polymers71,3902
Non-polymers3,32137
Water13,403744
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)149,42478
Polymers142,7814
Non-polymers6,64374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8910 Å2
ΔGint-32 kcal/mol
Surface area42890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.730, 60.880, 67.320
Angle α, β, γ (deg.)90.000, 94.870, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-403-

CS

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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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Details (production host): mutant beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42691.621 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): mutant Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 781 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#8: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#9: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 744 / 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: 2.63 Å3/Da / Density % sol: 53.27 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM bicine-CsOH, 8-10% PEG8000, 2-6 mM spermine, 1 mM DTT
PH range: 7.6-8.0 / Temp details: 295-299K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cobra - Oxford Cryosystems
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 26, 2017 / Details: VariMax HF
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→91.533 Å / Num. all: 81464 / Num. obs: 81464 / % possible obs: 90 % / Redundancy: 3.6 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.079 / Rsym value: 0.056 / Net I/av σ(I): 8.5 / Net I/σ(I): 10.5 / Num. measured all: 292658
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
1.64-1.733.60.2133.139739109720.1520.2960.2133.883.6
1.73-1.833.60.1524.337532105690.110.2120.1525.184.8
1.83-1.963.50.115.935383102240.0810.1570.116.787.3
1.96-2.123.40.0798.23374598490.060.1140.0798.890.2
2.12-2.323.50.0699.33230392230.0520.0980.06911.191.6
2.32-2.593.70.06210.33117585010.0460.0880.06212.993.3
2.59-2.993.80.062102849475820.0440.0850.06215.294.6
2.99-3.673.80.05411.12456165230.0380.0740.05418.395.7
3.67-5.193.70.03516.81922151350.0260.050.03520.196.6
5.19-37.293.60.03613.91050528860.030.0570.03618.697.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.566
Highest resolutionLowest resolution
Rotation37.29 Å1.83 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 81373
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.89-10033.90.923584
6.29-8.8941.10.9071053
5.13-6.2938.30.9021328
4.44-5.1328.20.9261583
3.98-4.4427.30.9311770
3.63-3.9826.20.9361935
3.36-3.63260.932088
3.14-3.3626.30.9312253
2.96-3.14250.9292392
2.81-2.9625.10.9252505
2.68-2.8124.50.9232585
2.57-2.6823.90.9292724
2.47-2.5724.40.9242808
2.38-2.4723.10.9342913
2.3-2.3821.90.9423017
2.22-2.321.40.9323090
2.16-2.2220.90.9353151
2.1-2.1621.70.943230
2.04-2.121.90.9283330
1.99-2.0422.40.9343365
1.94-1.9922.60.9163426
1.9-1.9423.30.9113414
1.85-1.923.80.9133477
1.81-1.85240.9173601
1.78-1.81240.9243530
1.74-1.7824.60.9143617
1.71-1.7424.50.9133685
1.68-1.7126.10.9083669
1.64-1.6834.30.8875250

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.6.02phasing
DM2.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CLL

2cll


Resolution: 1.64→37.32 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1838 / WRfactor Rwork: 0.1349 / FOM work R set: 0.8976 / SU B: 3.195 / SU ML: 0.049 / SU R Cruickshank DPI: 0.1179 / SU Rfree: 0.0853 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.175 4044 5 %RANDOM
Rwork0.1295 ---
obs0.1318 77328 89.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 21.925 Å2 / Biso min: 5.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.22 Å2
2--1.72 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: final / Resolution: 1.64→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 169 794 5959
Biso mean--31.85 34.1 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125419
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.657332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33922.119269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00615881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8071534
X-RAY DIFFRACTIONr_chiral_restr0.1030.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024085
X-RAY DIFFRACTIONr_rigid_bond_restr2.39535419
X-RAY DIFFRACTIONr_sphericity_free22.9445510
X-RAY DIFFRACTIONr_sphericity_bonded10.63455621
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 273 -
Rwork0.22 5262 -
all-5535 -
obs--83.15 %
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)
10.3554-0.0319-0.08490.66930.27020.12530.12680.09890.05770.0712-0.1055-0.00180.001-0.0708-0.02130.05870.0390.01640.13270.01880.1129-53.7863-3.460321.4728
20.2437-0.1427-0.05610.13950.01310.10350.0268-0.04580.0218-0.0224-0.0112-0.01330.0019-0.0435-0.01570.05370.01780.0090.1032-0.01170.1043-40.2678-6.287125.5996
30.96220.023-0.26770.8747-0.31280.1830.0270.1674-0.082-0.0352-0.0270.04780.0054-0.04440.00010.04970.0128-0.02820.116-0.01840.099-48.703-16.394810.972
40.4744-0.87770.07511.9035-0.23320.04490.14890.1472-0.0853-0.1025-0.18060.0511-0.0284-0.01180.03170.11750.083-0.08130.1265-0.02910.0687-52.5774-7.792710.2544
51.63021.7211.31176.41631.91741.12480.07660.07960.0312-0.1497-0.0714-0.11870.01610.0233-0.00520.0630.06230.04130.0770.04040.1218-38.20279.444812.8835
62.75872.96991.68963.32281.58031.60560.0122-0.02740.07690.05260.00330.0713-0.1577-0.1827-0.01550.09680.10220.02950.11030.04350.1359-49.88089.822213.9781
70.63440.0819-0.36320.0141-0.03860.2374-0.01340.0383-0.03260.0115-0.0054-0.0010.0372-0.07660.01890.0758-0.0298-0.02320.1173-0.00130.082-30.4691-28.872513.716
80.1688-0.0251-0.17280.00410.02560.2078-0.04620.0276-0.03280.0098-0.00560.00670.07920.01790.05180.10280.0146-0.01150.09840.00510.087-4.1258-33.68895.4563
90.0516-0.01020.05440.0052-0.02890.29130.00280.0304-0.0003-0.0013-0.0029-0.01240.0096-0.01640.00020.0871-0.0033-0.01230.0905-0.00440.0916-12.8978-24.713.2951
100.1325-0.09160.15030.0634-0.09980.34010.02460.01730.0275-0.019-0.013-0.0213-0.0738-0.0336-0.01160.08920.0145-0.00160.08320.00420.0969-14.3975-9.29962.5085
110.02370.0064-0.03890.0183-0.05480.2225-0.00960.0088-0.00220.00720.0007-0.00380.0376-0.04120.00890.0893-0.004-0.01590.08740.00020.0966-15.1328-27.430212.5463
120.01210.0167-0.01180.2863-0.02650.2207-0.008-0.02840.00570.01080.0002-0.00310.0139-0.02120.00780.0863-0.0007-0.00530.09-0.00670.101-8.7141-20.823426.1809
130.74150.68660.5250.95210.83130.83970.0295-0.04330.0115-0.0342-0.0089-0.0395-0.0004-0.0683-0.02060.0699-0.0070.00460.1053-0.01360.0919-23.5222-13.804625.7373
140.21020.0718-0.08970.2213-0.06450.21750.01340.01010.0155-0.00680.00450.00710.0167-0.0325-0.0180.0832-0.0032-0.00590.0858-0.00110.0933-14.0368-20.546922.428
150.2369-0.0991-0.07670.04480.01760.148-0.0079-0.00940.01610.01020.0136-0.0059-0.01130.017-0.00580.08330.0003-0.00760.0928-0.00220.09593.464-19.346819.6749
160.0117-0.01870.10250.0351-0.17981.03110.00230.022-0.0068-0.0106-0.0303-0.0061-0.03510.18130.0280.0777-0.0137-0.00490.11240.01410.09763.9836-17.325214.7829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 234
5X-RAY DIFFRACTION5A235 - 247
6X-RAY DIFFRACTION6A248 - 268
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 70
9X-RAY DIFFRACTION9B71 - 126
10X-RAY DIFFRACTION10B127 - 165
11X-RAY DIFFRACTION11B166 - 244
12X-RAY DIFFRACTION12B245 - 273
13X-RAY DIFFRACTION13B274 - 295
14X-RAY DIFFRACTION14B296 - 322
15X-RAY DIFFRACTION15B323 - 365
16X-RAY DIFFRACTION16B366 - 395

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