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- PDB-7jmq: The external aldimine form of the mutant beta-S377A Salmonella th... -

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Basic information

Entry
Database: PDB / ID: 7jmq
TitleThe external aldimine form of the mutant beta-S377A Salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the metal coordination site, and F9 inhibitor at the alpha-site. 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 / protein complex / F9F / internal aldimine
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-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 / 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. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Chem-F9F / Chem-KOU / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 external aldimine form of mutant beta-S377A Salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the ...Title: The external aldimine form of mutant beta-S377A Salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the metal coordination site, and F9 inhibitor at the alpha-site. 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
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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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)75,51245
Polymers71,6022
Non-polymers3,91043
Water14,304794
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)151,02490
Polymers143,2034
Non-polymers7,82186
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-41 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.380, 58.244, 67.154
Angle α, β, γ (deg.)90.000, 94.330, 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 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: 42902.879 Da / Num. of mol.: 1 / Mutation: S377A
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: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): beta-S377A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 837 molecules

#3: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: 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
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#6: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.48 Å3/Da / Density % sol: 50.46 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, 8% PEG 8,000, 6 mM Spermine, pH 7.6
PH range: 7.6-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cobra System / 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: Dec 7, 2019 / 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: 1.599→90.431 Å / Num. obs: 85831 / % possible obs: 93.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Rsym value: 0.043 / Net I/av σ(I): 9.9 / Net I/σ(I): 12.8
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
1.6-1.692.90.1325.131090106090.1010.1790.1326.179.4
1.69-1.793.10.1065.336573116890.0830.1480.1067.692.3
1.79-1.913.10.0797.434946111620.0640.1150.0799.693.4
1.91-2.073.10.0631032693104550.0520.0930.0631294.4
2.07-2.263.10.05211.93051697490.0420.0770.05214.395.6
2.26-2.533.10.0459.42809389710.0380.0690.04515.796.6
2.53-2.923.10.041152510279960.0350.0640.0411797.6
2.92-3.583.10.03514.12141668200.030.0540.0351998.4
3.58-5.063.10.0318.51671853640.0250.0450.0320.599.2
5.06-38.85830.03113.3915030160.0290.0510.03119.399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.387
Highest resolutionLowest resolution
Rotation38.86 Å1.73 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 85769
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.67-10032.40.926610
6.13-8.6741.20.8991101
5.01-6.13370.8931390
4.34-5.0128.80.9251638
3.88-4.3427.10.9391846
3.54-3.8828.30.9352038
3.28-3.54270.932204
3.07-3.2825.90.9312330
2.89-3.0727.60.9222517
2.74-2.8927.20.9182609
2.61-2.7424.60.9272745
2.5-2.6123.70.9242854
2.41-2.522.70.9272961
2.32-2.4122.50.9283073
2.24-2.3222.20.9243153
2.17-2.2420.90.9333263
2.1-2.1721.10.9323386
2.04-2.122.20.9283465
1.99-2.0421.80.9273489
1.94-1.99210.9273565
1.89-1.9421.80.9263691
1.85-1.8921.60.9233750
1.81-1.8521.60.9183803
1.77-1.8122.40.9213863
1.73-1.7722.10.9233968
1.7-1.7322.30.9153979
1.67-1.723.90.9184072
1.64-1.6727.60.8984043
1.6-1.6432.60.8934363

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Processing

Software
NameVersionClassification
xia2data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.1.002phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C73

6c73


Resolution: 1.6→38.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.498 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 4272 5 %RANDOM
Rwork0.1581 ---
obs0.1593 81498 92.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.39 Å2 / Biso mean: 15.347 Å2 / Biso min: 4.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.02 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.6→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 200 833 6050
Biso mean--30.24 29.91 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125453
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.6317376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93522.243263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78215881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2891535
X-RAY DIFFRACTIONr_chiral_restr0.0970.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024171
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 236 -
Rwork0.177 4442 -
all-4678 -
obs--68.7 %
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)
10.13880.01420.15640.25770.03610.3077-0.00420.0459-0.00690.0034-0.01140.007-0.0210.02270.01560.0157-0.00420.00150.0296-0.00040.021537.8089.98878.9392
20.4492-0.3471-0.26790.76330.37730.4734-0.0127-0.0094-0.09030.08010.03330.02190.06170.0023-0.02070.0234-0.0033-0.01360.00570.00310.041747.0062-1.798321.627
30.5089-0.0280.33170.2694-0.0210.2165-0.07570.02640.05610.05460.0364-0.0245-0.04940.01710.03920.039-0.0055-0.01260.01210.00540.034147.789116.04622.5637
40.65080.1049-0.11210.0445-0.10460.37310.01470.0357-0.0957-0.0134-0.019-0.02820.05770.09550.00440.02310.0155-0.0040.0318-0.00950.052527.9395-13.350919.1205
50.3685-0.11540.03030.0986-0.08890.2814-0.001-0.0558-0.02470.00550.0111-0.00730.0596-0.0757-0.01010.0271-0.03-0.0070.04160.01260.02171.3834-17.796827.7579
60.09370.07390.1130.14470.05030.15550.0095-0.0141-0.00680.0228-0.0053-0.01820.0039-0.0255-0.00420.02840.0007-0.00240.02290.00560.023110.585-8.908330.1184
70.11350.23870.02040.5812-0.17980.9520.0152-0.00620.01790.0264-0.00330.0244-0.07120.0029-0.0120.0307-0.00730.01410.0067-0.00260.023914.09816.802932.0037
80.12260.07170.02240.0920.08150.15180.00310.0066-0.011-0.0009-0.0046-0.00540.02450.01820.00140.030.0054-0.0030.02160.00330.026212.8695-11.565321.0647
90.120.06980.00730.0914-0.08350.1623-0.00940.03750.012-0.00410.00580.0043-0.00350.02190.00360.0184-0.00010.00260.02180.00610.027611.8986-0.07188.9233
100.1917-0.0054-0.01890.007-0.0290.1812-00.0150.0062-0.00040.0075-0.0025-0.004-0.0155-0.00750.0184-0.00160.00480.0219-0.00140.024-0.2035-4.538212.9815
110.38150.10280.19230.64730.20140.80320.0517-0.00590.02370.06930.0442-0.0089-0.0382-0.0595-0.09590.03270.00910.02530.01060.00710.0292-7.3948-0.421118.1303
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 - 126
7X-RAY DIFFRACTION7B127 - 165
8X-RAY DIFFRACTION8B166 - 244
9X-RAY DIFFRACTION9B245 - 301
10X-RAY DIFFRACTION10B302 - 364
11X-RAY DIFFRACTION11B365 - 397

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