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- PDB-7l47: The internal aldimine form of the beta-K167T mutant Tryptophan Sy... -

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Basic information

Entry
Database: PDB / ID: 7l47
TitleThe internal aldimine form of the beta-K167T mutant Tryptophan Synthase from Salmonella at 1.55 Angstrom resolution with cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / internal aldimine
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
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
: / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 beta-K167T mutant Tryptophan Synthase from Salmonella at 1.55 Angstrom resolution with cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 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)74,30439
Polymers71,5902
Non-polymers2,71437
Water12,701705
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)148,60878
Polymers143,1794
Non-polymers5,42974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area23120 Å2
ΔGint-291 kcal/mol
Surface area43130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.979, 59.330, 67.070
Angle α, β, γ (deg.)90.000, 94.340, 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: 42890.805 Da / Num. of mol.: 1 / Mutation: K167T
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): K167T / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 742 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.58 Å3/Da / Density % sol: 52.34 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM Spermine, pH 7.6
PH range: 7.60-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / 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: Mar 5, 2020 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→90.729 Å / Num. obs: 99916 / % possible obs: 96.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.05 / Rrim(I) all: 0.091 / Rsym value: 0.06 / Net I/av σ(I): 9.8 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.55-1.632.20.5511.3115820.4770.7680.55177.3
1.63-1.7330.4321.7141680.3240.5890.43299.7
1.73-1.853.10.2882.6134070.2170.3960.288100
1.85-23.10.1764.2124340.1360.2490.176100
2-2.193.20.1077115090.0840.1550.107100
2.19-2.453.20.0759.7103980.060.1110.075100
2.45-2.833.20.05712.392030.0480.0880.057100
2.83-3.473.30.0471377770.0380.0720.04799.9
3.47-4.93.30.0281260620.0250.0460.02899.9
4.9-103.20.0242033760.0270.050.02499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.68 Å38.94 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 99859
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.4-10030.40.906688
5.94-8.439.20.8881211
4.85-5.9433.70.9111570
4.2-4.8525.70.9341848
3.76-4.2260.9242089
3.43-3.7624.40.9432298
3.18-3.4324.60.9322501
2.97-3.1825.10.9242687
2.8-2.9724.70.9152831
2.66-2.823.30.923030
2.53-2.6622.80.9243177
2.43-2.5322.20.9233302
2.33-2.4320.90.9293440
2.25-2.3320.60.9313567
2.17-2.2520.90.9293715
2.1-2.1720.10.9373820
2.04-2.121.20.9313915
1.98-2.0422.20.9224070
1.93-1.9822.70.9164221
1.88-1.9323.80.9144278
1.83-1.8824.60.9114399
1.79-1.8326.30.9074459
1.75-1.79280.9074625
1.72-1.7529.30.9024698
1.68-1.7232.30.8994797
1.65-1.6836.20.8934888
1.62-1.6539.60.8724803
1.59-1.6244.30.864156
1.55-1.5947.30.8374776

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K0B

7k0b


Resolution: 1.55→38.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.969 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0865 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 5064 5.1 %RANDOM
Rwork0.1878 ---
obs0.1891 94796 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.36 Å2 / Biso mean: 23.514 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0.07 Å2
2--0.29 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.55→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4879 0 124 727 5730
Biso mean--40.53 36.66 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125266
X-RAY DIFFRACTIONr_angle_refined_deg1.591.6327128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39622.568257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70915855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7321532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024051
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 240 -
Rwork0.393 4849 -
all-5089 -
obs--67.07 %
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)
10.32280.06070.21770.36030.09530.4317-0.01040.0177-0.0116-0.0063-0.0134-0.0101-0.0471-0.02560.02380.02280.00490.01320.08830.00780.03638.55110.4419.335
20.63460.09060.41943.11131.24550.73740.0561-0.0119-0.14460.19810.0588-0.04430.10510.0296-0.11490.03120.0024-0.01060.08150.00680.065249.475-2.72619.245
32.4162-1.36741.53851.3789-0.37761.3867-0.1571-0.06870.0830.11540.02390.0107-0.1142-0.06130.13310.0378-0.0058-0.02880.11060.00130.032247.37119.4722.534
40.7305-0.0356-0.33330.0803-0.11020.37360.02580.0244-0.0297-0.0406-0.0548-0.01490.06110.12270.0290.02940.0345-0.00460.1468-0.01460.024927.81-13.0419.383
50.3609-0.15020.05610.1185-0.170.433-0.0365-0.0732-0.0238-0.01080.0395-0.00170.0788-0.1032-0.0030.0322-0.0157-0.01260.1170.01240.02671.356-17.53327.736
60.5813-0.0230.46910.0882-0.00280.3842-0.0051-0.0293-0.01560.00130.025-0.02240.0036-0.0335-0.01990.039-0.0042-0.00380.12710.00170.016.136-11.84227.669
70.01350.02480.0260.9424-0.35970.7510.040.02070.00860.0596-0.0048-0.0076-0.0635-0.0167-0.03520.06310.02970.03420.12050.01050.022615.943.61233.611
80.06090.02980.00780.04510.07340.2140.0160.03070.01140.0174-0.0023-0.00160.04220.0288-0.01370.03070.00530.00050.12420.00280.025411.254-9.89318.486
91.6104-0.02890.0960.2148-0.31790.4730.08060.03170.1437-0.0198-0.05240.01880.03320.0646-0.02820.0093-0.01010.00960.11640.00990.050616.5683.2088.901
100.3884-0.026-0.14870.0028-0.00660.39750.01110.00250.0415-0.00090.0024-0.0050.0039-0.0119-0.01350.0233-0.00370.00530.1213-0.00170.0277-0.281-4.28612.953
110.26910.18070.05390.30780.33621.13470.0528-0.00340.01490.04050.01950.0183-0.0859-0.0376-0.07240.04420.00110.02450.11840.00790.0164-7.015-0.70417.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 159
2X-RAY DIFFRACTION2A160 - 216
3X-RAY DIFFRACTION3A217 - 267
4X-RAY DIFFRACTION4B2 - 37
5X-RAY DIFFRACTION5B38 - 70
6X-RAY DIFFRACTION6B71 - 100
7X-RAY DIFFRACTION7B101 - 165
8X-RAY DIFFRACTION8B166 - 269
9X-RAY DIFFRACTION9B270 - 301
10X-RAY DIFFRACTION10B302 - 364
11X-RAY DIFFRACTION11B365 - 396

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