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- PDB-7kxc: The aminoacrylate form of the wild-type Salmonella typhimurium Tr... -

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Basic information

Entry
Database: PDB / ID: 7kxc
TitleThe aminoacrylate 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, sodium ion at the metal coordination site and benzimidazole (BZI) at the enzyme beta-site at 1.30 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Inhibitor / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / 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 / 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-0JO / BENZIMIDAZOLE / Chem-F9F / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 1.51 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 aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme ...Title: The aminoacrylate 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, sodium ion at the metal coordination site and benzimidazole (BZI) at the enzyme beta-site at 1.30 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 3, 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)73,16015
Polymers71,6182
Non-polymers1,54313
Water12,665703
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 area5290 Å2
ΔGint-11 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.130, 59.359, 67.477
Angle α, β, γ (deg.)90.000, 95.160, 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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA, DD95_04145 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: A0A0D6FWC1, 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: 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, 716 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BZI / BENZIMIDAZOLE / Benzimidazole


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.59 Å3/Da / Density % sol: 52.48 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 9% 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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.509→91.691 Å / Num. obs: 112796 / % possible obs: 99.2 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.035 / Rrim(I) all: 0.111 / Rsym value: 0.098 / Net I/av σ(I): 5.2 / Net I/σ(I): 10.4
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
1.51-1.5970.551112970161850.250.6610.552.298.3
1.59-1.699.90.5691.1153012154740.20.6380.5693.298.7
1.69-1.810.50.3871.6152782145370.1340.4360.3874.699.1
1.8-1.9510.30.2572.3140366135870.0920.2950.2576.899.3
1.95-2.1410.30.1733.3129858125860.0620.1980.17310.399.5
2.14-2.39100.1364.2113586113760.0490.1550.13613.399.8
2.39-2.769.50.1095.696302100950.0390.1240.10915.799.8
2.76-3.3810.80.0787.99219385660.0260.0850.07821.9100
3.38-4.7810.90.05112.17300566690.0170.0560.05130.399.9
4.78-39.566100.03914.43729337210.0140.0440.03928.699.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.62
Highest resolutionLowest resolution
Rotation39.57 Å1.73 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 111873
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.18-10034.20.891745
5.79-8.1837.80.8971360
4.73-5.7929.50.921726
4.09-4.7323.70.9382042
3.66-4.0923.50.9322298
3.34-3.6622.50.9272527
3.09-3.3423.90.9052749
2.89-3.0924.40.8952952
2.73-2.8923.20.8933115
2.59-2.7323.40.8893308
2.47-2.5922.50.8843426
2.36-2.4722.40.883587
2.27-2.3620.90.8823757
2.19-2.2720.40.8753860
2.11-2.1921.60.8744043
2.05-2.1121.10.8624107
1.98-2.0521.80.8644275
1.93-1.9821.20.8694422
1.88-1.9322.40.8584481
1.83-1.8824.10.8544585
1.79-1.8324.40.844776
1.74-1.7925.20.8334830
1.71-1.7425.10.8474946
1.67-1.7125.90.8475039
1.64-1.6726.30.8395115
1.61-1.6427.60.8495274
1.58-1.6128.70.8455394
1.55-1.5829.20.8355459
1.51-1.5536.20.8027675

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Processing

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

4ht3


Resolution: 1.51→39.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.249 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0825 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 5503 4.9 %RANDOM
Rwork0.1982 ---
obs0.1998 106370 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.57 Å2 / Biso mean: 22.291 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2---0.05 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.51→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 100 715 5771
Biso mean--30.15 35.55 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125389
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6347325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74122.424264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4761533
X-RAY DIFFRACTIONr_chiral_restr0.110.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024229
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 396 -
Rwork0.272 7770 -
all-8166 -
obs--97.47 %
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)
10.41010.14140.00850.33850.00330.03770.02860.02940.0161-0.0014-0.0285-0.0415-0.00830.017-0.00010.0439-0.01840.01270.03980.02060.096137.49829.86088.4236
20.7006-0.1728-0.4441.28670.21320.68330.0677-0.2279-0.13040.0999-0.0919-0.2125-0.06760.13670.02430.0259-0.0341-0.050.09280.06370.134445.7817-0.342822.4824
31.19160.0092-0.22010.3819-0.11460.10720.0926-0.21730.03810.0953-0.08610.028-0.05340.1073-0.00650.0485-0.0494-0.02850.1120.0010.088346.151517.439822.2627
41.0859-0.2549-0.47580.09080.08360.2656-0.0059-0.0636-0.0934-0.0111-0.0379-0.01520.01980.11760.04370.04370.0228-0.01360.1480.02970.087727.6057-13.045320.1423
50.15350.0663-0.18380.0929-0.18930.4348-0.0862-0.0444-0.0282-0.01780.0171-0.04440.0874-0.05870.06910.0740.0052-0.01560.10070.00720.04121.0899-17.747128.1244
60.19390.0961-0.1240.0583-0.02650.29850.0303-0.041-0.00850.0084-0.02410.007-0.01530.0518-0.00620.0806-0.01-0.01640.06320.00540.050711.3679-6.447826.3434
70.43970.0918-0.02420.0450.04150.12710.00380.03410.03580-0.0080.0015-0.00840.01370.00420.0771-0.004-0.00680.05220.01510.068211.8201-0.41638.5601
80.492-0.0099-0.18130.0251-0.00370.30560.00440.00280.0123-0.00250.00210.0013-0.0079-0.0198-0.00660.07620.0016-0.01390.06010.00210.0479-0.1805-4.74212.8737
90.15940.21440.14650.3040.20231.15150.0442-0.0228-0.020.0341-0.0107-0.0322-0.1225-0.2247-0.03360.09440.03190.00480.0949-0.00430.0193-6.8286-2.43717.9703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 202
3X-RAY DIFFRACTION3A203 - 268
4X-RAY DIFFRACTION4B2 - 37
5X-RAY DIFFRACTION5B38 - 70
6X-RAY DIFFRACTION6B71 - 244
7X-RAY DIFFRACTION7B245 - 301
8X-RAY DIFFRACTION8B302 - 364
9X-RAY DIFFRACTION9B365 - 394

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