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- PDB-7kqf: The internal aldimine form of the wild-type Tryptophan Synthase f... -

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Basic information

Entry
Database: PDB / ID: 7kqf
TitleThe internal aldimine form of the wild-type Tryptophan Synthase from Salmonella in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.47 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / inhibitor / LYASE / 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. / 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-F9F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 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 Tryptophan Synthase from Salmonella in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme ...Title: The internal aldimine form of the wild-type Tryptophan Synthase from Salmonella in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.47 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionNov 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 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

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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)73,93825
Polymers71,6182
Non-polymers2,32023
Water14,088782
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 area7210 Å2
ΔGint-138 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.851, 58.561, 67.183
Angle α, β, γ (deg.)90.000, 94.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-986-

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
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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 805 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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.11 Å3/Da / Density % sol: 51.05 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
PH range: 7.8-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2020 / Details: Osmic Varimax HF ArcSec
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.469→90.63 Å / Num. obs: 103254 / % possible obs: 86.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Rsym value: 0.056 / Net I/av σ(I): 8.2 / Net I/σ(I): 9.4
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
1.47-1.5520.1783.6969848940.2550.3690.1782.728.4
1.55-1.642.40.138530040125360.1310.2090.1383.576.2
1.64-1.763.50.1364.953192153990.0950.1790.1365.499.4
1.76-1.93.50.107650565144040.0730.1380.1077.399.8
1.9-2.083.60.0867.247444133250.0580.1090.0869.7100
2.08-2.323.60.0748.343629120560.0480.0920.07411.9100
2.32-2.683.70.0649.339022106550.0420.0820.06413.2100
2.68-3.293.70.05510.63344590250.0370.0710.05514.8100
3.29-4.653.70.04213.82622570260.0290.0560.04216.3100
4.65-39.0163.70.03316.11446339340.0270.0520.03316.399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.382
Highest resolutionLowest resolution
Rotation39.02 Å1.69 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 103241
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.97-10031.90.906795
5.63-7.9736.70.9081426
4.6-5.6329.80.9241835
3.98-4.624.20.9462133
3.56-3.9823.30.9322411
3.25-3.5623.20.9212679
3.01-3.2523.40.9262913
2.82-3.0124.90.9123095
2.66-2.8222.40.9253303
2.52-2.6622.20.9343494
2.4-2.5221.90.9333651
2.3-2.421.10.9333835
2.21-2.320.30.9364002
2.13-2.2119.60.9434151
2.06-2.1318.90.9384286
1.99-2.0619.60.9314449
1.93-1.9919.50.9424547
1.88-1.9319.60.9424691
1.83-1.8820.40.9354832
1.78-1.8321.10.9364960
1.74-1.7821.70.9375079
1.7-1.7422.20.935189
1.66-1.723.70.9275250
1.63-1.6625.50.9225207
1.59-1.6326.80.924734
1.56-1.5928.50.9083898
1.53-1.5628.80.9012939
1.51-1.5333.70.8442054
1.47-1.5138.50.8181403

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Processing

Software
NameVersionClassification
xia2XIA2 0.5.902data 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: 1.47→39.02 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.369 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0738 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 5042 4.9 %RANDOM
Rwork0.1231 ---
obs0.1249 98200 86.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.92 Å2 / Biso mean: 19.022 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20.76 Å2
2---0.78 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.47→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4992 0 111 798 5901
Biso mean--32.11 36.08 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125507
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.6337481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86522.193269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66815911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1891536
X-RAY DIFFRACTIONr_chiral_restr0.090.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024295
X-RAY DIFFRACTIONr_rigid_bond_restr1.99935506
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 69 -
Rwork0.262 1488 -
all-1557 -
obs--17.74 %
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)
10.01050.00250.00070.01660.00420.0068-0.00010.0005-0.0003-0.00050.00010.0002-0.0006-0.00050.00010.0020.0001-0.00370.009200.007137.18238.04068.6776
20.0609-0.0364-0.03870.06520.03260.0651-0.0018-0.0063-0.00090.00310.0023-0.00080.00390.0065-0.00050.00220-0.00380.010.00020.007147.057-1.695121.5742
30.0204-0.01250.00480.03010.00190.00380.0003-0.00260.0006-0.00150.0015-0.00120.0003-0.0006-0.00170.0017-0-0.00330.00920.00030.006946.936412.073522.9962
40.5093-0.39770.11870.393-0.0730.0865-0.0070.00660.02610.0074-0.0013-0.0245-0.0046-00.00830.0018-0.0008-0.00310.00850.00040.006149.36224.23221.1567
50.02930.0117-0.00580.0174-0.01830.04050.0012-0.0005-0.0003-0.0006-0.0007-0.00110.00360.0022-0.00040.00190.0002-0.00340.0086-0.00030.007527.7251-13.147619.3417
60.0518-0.01850.03490.0072-0.01590.04220.001-0.0037-0.0042-0.00050.00130.00160.0012-0.0021-0.00230.0018-0.0001-0.00360.0082-0.00010.00771.2761-17.772727.7046
70.00470.00220.00390.00720.0060.0117-0.0005-0.00120.0009-0.00020.0006-0.0002-0.00110.0002-0.00010.00210.0001-0.00380.0091-00.007510.4083-8.697730.2015
80.04210.0172-0.00080.0463-0.06290.09970.0015-0.00050.00280.0023-0.00040.0019-0.00290.0003-0.00110.00210.0002-0.00360.0084-0.0010.007114.13627.071132.2746
90.01630.00970.00370.00820.00120.00820.00060.0009-0.00090.00060.0001-0.00060.00080.0006-0.00070.00190.0002-0.00370.009-0.00010.007512.7679-11.405421.1442
100.02180.0064-0.00280.0024-0.00210.006-0.00060.00050.00080.00060.0004-0.0009-0.0007-0.00050.00020.0019-0.0001-0.00360.009100.007211.8220.01569.0263
110.0301-0.0126-0.01770.00870.00570.0323-0.00060.00240.0003-0.00010.00020.0003-0-0.00110.00050.0021-0.0002-0.00390.00840.00010.00732.4395-4.333812.5449
120.01310.01810.02070.04470.01990.0751-0.002-0.00190.0005-0.0012-0.00060.001-0.0073-0.00330.00260.00220.0006-0.00350.0092-0.00010.0076-6.5261-3.019316.3519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 159
2X-RAY DIFFRACTION2A160 - 202
3X-RAY DIFFRACTION3A203 - 247
4X-RAY DIFFRACTION4A248 - 268
5X-RAY DIFFRACTION5B2 - 37
6X-RAY DIFFRACTION6B38 - 70
7X-RAY DIFFRACTION7B71 - 126
8X-RAY DIFFRACTION8B127 - 165
9X-RAY DIFFRACTION9B166 - 244
10X-RAY DIFFRACTION10B245 - 301
11X-RAY DIFFRACTION11B302 - 343
12X-RAY DIFFRACTION12B344 - 394

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