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

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Basic information

Entry
Database: PDB / ID: 7lev
TitleThe aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with ammonium ion at the metal coordination site at 1.70 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE
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 / AMMONIUM ION / 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: 1.7 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 ammonium ion at the metal coordination site at 1.70 Angstrom resolution.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionJan 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: 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)72,94020
Polymers71,6182
Non-polymers1,32318
Water7,855436
1


  • Idetical with deposited unit
  • defined by 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 area4720 Å2
ΔGint-24 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.389, 59.610, 67.230
Angle α, β, γ (deg.)90.000, 95.010, 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 , 6 types, 454 molecules

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


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / 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-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.56 Å3/Da / Density % sol: 51.87 % / 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 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→91.344 Å / Num. obs: 78296 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Rsym value: 0.073 / Net I/av σ(I): 6 / Net I/σ(I): 7
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
1.7-1.793.50.3162.139806115190.250.4680.3162.399.5
1.79-1.93.40.2482.737311108450.1980.3690.248399.4
1.9-2.033.40.164435223102510.1240.2320.1644.799.3
2.03-2.193.40.1145.73252695350.0850.160.1146.699.3
2.19-2.43.30.0897.12941387920.0650.1220.0897.899.4
2.4-2.693.30.0728.32652179710.0520.0980.0729.199.5
2.69-3.13.10.0629.32179170310.0450.0820.06210.599.7
3.1-3.82.80.05810.61687459880.0430.0750.0581299.6
3.8-5.383.50.05611.41521443840.0360.0680.05614.194.2
5.38-29.0863.20.0511.8640719800.0310.0580.0513.175.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.511
Highest resolutionLowest resolution
Rotation29.09 Å1.93 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 78242
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.31-10053.70.836527
5.73-7.3141.60.8741025
4.86-5.7335.90.8971245
4.3-4.8628.50.9241406
3.9-4.325.80.9251636
3.59-3.920.90.9311848
3.35-3.5920.90.9262012
3.14-3.3520.80.9212146
2.98-3.1420.30.9142247
2.83-2.9821.80.9022369
2.71-2.8320.20.9122514
2.6-2.7121.40.9052584
2.5-2.620.50.9012689
2.41-2.522.10.8882801
2.33-2.4121.30.8962892
2.26-2.3321.10.8932993
2.2-2.2620.80.9043055
2.14-2.221.20.9063125
2.08-2.1420.90.9143299
2.03-2.0822.10.913306
1.98-2.0323.20.8953383
1.94-1.9825.10.8883522
1.9-1.9426.10.8813584
1.86-1.926.30.8723587
1.82-1.8627.80.873687
1.79-1.82290.8683814
1.75-1.7929.10.873837
1.7-1.7535.10.8327109

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WDU

6wdu


Resolution: 1.7→29.09 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 3811 4.87 %
Rwork0.206 74428 -
obs0.2079 78239 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.97 Å2 / Biso mean: 40.1163 Å2 / Biso min: 14.64 Å2
Refinement stepCycle: final / Resolution: 1.7→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 71 447 5116
Biso mean--51.26 44.56 -
Num. residues----626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.31621890.28273766395599
1.73-1.760.31131830.27763747393099
1.76-1.790.30671940.28113721391599
1.79-1.830.32321880.27453718390699
1.83-1.870.34051820.28223763394599
1.87-1.910.30021960.26173759395599
1.91-1.960.28862020.23983726392899
1.96-2.020.27862030.24083711391499
2.02-2.070.27641910.23413733392499
2.07-2.140.25021700.22823805397599
2.14-2.220.24861730.22423731390499
2.22-2.310.26191990.2193792399199
2.31-2.410.27652180.21673708392699
2.41-2.540.23361990.21573741394099
2.54-2.70.23281940.20283786398099
2.7-2.910.24981800.204237893969100
2.91-3.20.24521990.19453777397699
3.2-3.660.23911760.176237973973100
3.66-4.610.21452030.16173687389096
4.61-29.090.20451720.2033171334381
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)
10.0369-0.02470.02810.0786-0.01880.14880.3696-0.18480.24880.4041-0.3354-0.1781-0.38160.34030.00780.3908-0.15010.02060.34450.07330.577251.296312.555311.7746
20.0953-0.02820.11010.0185-0.01250.095-0.0238-0.32710.54230.6508-0.15060.305-0.79650.0833-0.04490.591-0.3980.2519-1.4342-0.31140.736.125718.287513.6281
30.13550.0906-0.06990.1122-0.03840.14710.2529-0.03350.25980.0245-0.12990.0471-0.16370.10680.05550.256-0.010.07390.13610.05490.350138.01928.7194.5003
40.2064-0.2283-0.15190.31730.20080.27160.1264-0.0846-0.4105-0.0284-0.2986-0.62030.01270.2183-0.12660.2297-0.0585-0.06460.21810.13190.473246.2846-3.598713.9241
5-0.0086-0.0076-0.00040.03490.00320.05030.173-0.29130.1070.2573-0.21610.0113-0.2890.15040.01750.5428-0.1174-0.00060.434-0.13620.544746.432215.409824.2291
60.01580.0123-0.02690.0168-0.01530.06650.0956-0.1120.10130.059-0.12860.0428-0.26830.1112-0.00361.0925-0.36690.02430.5165-0.31410.844249.387424.174720.428
70.3220.2438-0.4430.1874-0.06340.6431-0.0116-0.1762-0.15030.0354-0.0751-0.0382-0.02580.05670.00010.170.0006-0.02850.21570.03780.158512.23-13.702824.5394
80.58520.26210.08970.2457-0.04610.16980.82960.08530.1327-0.20310.14-0.1023-0.87280.16150.30090.5229-0.06190.24220.3988-0.010.158316.70210.615733.1282
90.7539-0.012-0.4340.1350.21730.56790.0554-0.00620.0986-0.0456-0.09130.02710.00010.02-00.18150.0086-0.02850.19680.02150.16629.6723-10.480215.7782
100.522-0.4866-0.23340.3528-0.20040.12660.06190.08880.23480.0057-0.008-0.1025-0.0905-0.0870.00070.19320.01320.00080.21950.00830.177-0.1246-1.631713.78
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A1 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 77 )A30 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 136 )A78 - 136
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 210 )A137 - 210
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 247 )A211 - 247
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 268 )A248 - 268
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 100 )B2 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 179 )B101 - 179
9X-RAY DIFFRACTION9chain 'B' and (resid 180 through 286 )B180 - 286
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 395 )B287 - 395

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