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- PDB-7kmc: The internal aldimine crystal structure of the beta-K167T mutant ... -

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Basic information

Entry
Database: PDB / ID: 7kmc
TitleThe internal aldimine crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-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 / 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
: / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 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)73,90333
Polymers71,5902
Non-polymers2,31331
Water13,115728
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Tryptophan Synthase complex (alpha2-beta2) Protein is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-85 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.620, 59.230, 67.150
Angle α, β, γ (deg.)90.000, 94.520, 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, 759 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: 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
#8: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 52.5 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 4 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: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→91.026 Å / Num. obs: 111333 / % possible obs: 97.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.067 / Rrim(I) all: 0.155 / Rsym value: 0.133 / Net I/av σ(I): 3.1 / Net I/σ(I): 5.4
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
1.5-1.585.10.8730.582511162200.4411.0080.8732.297.8
1.58-1.684.60.5350.970111152500.2850.6250.5352.896.8
1.68-1.795.20.3541.574673144680.1810.4150.3543.897.8
1.79-1.945.20.2651.870696135030.1350.3110.2654.998.1
1.94-2.124.70.1772.757818122140.0960.2130.177696.1
2.12-2.375.30.1463.660140112600.0730.170.1467.498.1
2.37-2.745.30.124.35302099400.060.140.128.298.2
2.74-3.354.80.1055.13940382570.0540.1240.1058.495.9
3.35-4.745.50.096.13629166330.0430.1040.099.899
4.74-39.0985.10.0616.81817835880.030.0720.0619.295.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.69 Å39.1 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 111331
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.13-100310.903769
5.75-8.1338.20.8821324
4.69-5.7531.30.9141613
4.07-4.6924.40.9312009
3.64-4.07250.9362303
3.32-3.6423.60.9392512
3.07-3.3225.50.9262765
2.87-3.0725.90.9192718
2.71-2.8724.80.9293026
2.57-2.71240.9263262
2.45-2.57240.9183432
2.35-2.4523.70.9233583
2.26-2.3522.20.9283759
2.17-2.2622.50.9233885
2.1-2.1722.10.9283907
2.03-2.122.70.9274009
1.97-2.0323.60.9124277
1.92-1.9722.70.9194367
1.87-1.92230.914517
1.82-1.8723.80.9174669
1.77-1.8224.70.9144778
1.73-1.7724.90.9024896
1.7-1.7327.40.8934989
1.66-1.7290.8884898
1.63-1.6628.50.895143
1.59-1.6329.20.8935285
1.56-1.5929.20.8945389
1.54-1.5629.90.8935513
1.5-1.54370.8397734

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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: 1.5→39.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.301 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0815 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 5590 5 %RANDOM
Rwork0.1533 ---
obs0.1555 105741 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.86 Å2 / Biso mean: 22.209 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.15 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.5→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 115 764 5802
Biso mean--39.72 36.18 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125417
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.6357346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60522.259270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94715893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7241536
X-RAY DIFFRACTIONr_chiral_restr0.0950.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024217
X-RAY DIFFRACTIONr_rigid_bond_restr1.89735417
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 430 -
Rwork0.23 7778 -
all-8208 -
obs--97.89 %
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)
10.46750.12120.39030.33960.1040.9194-0.1361-0.00760.02430.01460.0349-0.0126-0.1107-0.10450.10120.05820.01540.00810.0269-0.00160.045836.441718.019910.9256
20.53580.5957-0.16130.9942-0.41890.27790.05020.0067-0.01850.0054-0.03750.001-0.02070.0194-0.01270.04780.01230.01020.0145-0.00610.034938.92992.65796.71
31.35510.6799-0.37042.1665-0.16440.72150.0799-0.1001-0.12420.0162-0.0689-0.10150.06840.1054-0.0110.0362-0.0056-0.04080.02470.02130.057446.7398-4.752617.2185
40.658-0.69170.16724.3811.08550.4793-0.0983-0.0191-0.12590.39330.2019-0.0230.08610.0681-0.10360.05750.0324-0.0060.0422-0.01210.067452.0452-0.818422.0065
51.2485-0.39211.22860.46-0.21351.2997-0.1158-0.08480.08080.08280.0189-0.0417-0.1178-0.09470.09680.05580.0016-0.0310.0144-0.0020.041247.579119.724422.5844
60.2825-0.02050.05110.0068-0.0340.2676-0.0003-0.0209-0.0190.00070.0036-0.00560.0303-0.0104-0.00330.03370.0037-0.01530.02770.00110.029612.4327-14.192524.7061
70.5159-0.4673-0.5611.38740.00230.9250.18310.09810.1079-0.0234-0.0416-0.0718-0.1963-0.1199-0.14140.12190.03620.01020.03660.01630.039614.90052.155534.0196
80.16190.0084-0.00160.0042-0.02460.21310.00980.02840.03490.002-0.0055-0.00060.01240.0124-0.00430.0297-0.0031-0.00620.0360.00360.03349.0638-4.98716.1786
90.26220.0758-0.12930.06880.15480.90210.0550.0370.0215-0.00590.036-0.0109-0.11460.0211-0.0910.0570.00340.01270.04750.00880.013-7.0455-0.703617.7495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 91
2X-RAY DIFFRACTION2A92 - 159
3X-RAY DIFFRACTION3A160 - 192
4X-RAY DIFFRACTION4A193 - 216
5X-RAY DIFFRACTION5A217 - 268
6X-RAY DIFFRACTION6B2 - 100
7X-RAY DIFFRACTION7B101 - 151
8X-RAY DIFFRACTION8B152 - 364
9X-RAY DIFFRACTION9B365 - 396

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