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- PDB-7kq9: The aminoacrylate form of the beta-Q114A mutant Tryptophan Syntha... -

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Basic information

Entry
Database: PDB / ID: 7kq9
TitleThe aminoacrylate form of the beta-Q114A 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 / 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-0JO / BROMIDE ION / : / DI(HYDROXYETHYL)ETHER / SERINE / 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 aminoacrylate form of the beta-Q114A 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 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 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)73,64526
Polymers71,5612
Non-polymers2,08524
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&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 area6270 Å2
ΔGint-126 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.622, 59.920, 67.416
Angle α, β, γ (deg.)90.000, 94.870, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-812-

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: 42861.828 Da / Num. of mol.: 1 / Mutation: Q114A
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): Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 615 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: 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
#9: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#10: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.33 Å3/Da / Density % sol: 0.47 % / 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: 7.6-8.00 / 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: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.499→90.982 Å / Num. obs: 114154 / % possible obs: 98.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Rsym value: 0.069 / Net I/av σ(I): 5 / Net I/σ(I): 10.1
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
1.5-1.586.30.4781.3103928164300.220.5590.4782.397.6
1.58-1.686.70.3232104752156620.1430.3730.3233.398.2
1.68-1.796.30.2152.993325147400.0990.2510.2154.598.2
1.79-1.946.60.1673.590695137530.0740.1930.1676.898.2
1.94-2.126.80.1125.386134127420.050.1290.1129.899
2.12-2.376.30.0916.371865114460.0420.1060.0911398
2.37-2.7470.078.672066102970.0310.0810.0716.999.5
2.74-3.356.40.06105505785750.0270.0690.0620.798
3.35-4.746.90.0511.74713867960.0220.0570.0526.899.8
4.74-39.2456.60.0519.42450637130.0230.0590.05126.497.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.71 Å39.24 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 113634
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.13-10033.80.915782
5.75-8.1339.40.8891311
4.69-5.7531.40.9141746
4.07-4.6922.90.9372076
3.64-4.0721.60.9312337
3.32-3.6422.60.9252566
3.07-3.32230.922691
2.87-3.07250.9172996
2.71-2.8723.50.9133175
2.57-2.7123.50.9083366
2.45-2.5724.60.8993533
2.35-2.4523.70.9033673
2.25-2.3523.40.8943683
2.17-2.2522.50.9013949
2.1-2.1722.90.8994130
2.03-2.124.10.8974281
1.97-2.0325.60.8784362
1.92-1.9725.90.8544443
1.87-1.9225.50.8684589
1.82-1.8726.20.8674704
1.77-1.8228.80.8584739
1.73-1.7728.40.8734929
1.7-1.7328.60.875063
1.66-1.730.40.8655138
1.63-1.6630.20.8675283
1.59-1.6332.60.875396
1.56-1.5932.10.8665449
1.54-1.5635.50.8465522
1.5-1.5442.70.7797722

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Processing

Software
NameVersionClassification
xia2data 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: 6VFD

6vfd


Resolution: 1.5→39.28 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.6 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 5768 5.1 %RANDOM
Rwork0.1776 ---
obs0.1796 107867 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 233.77 Å2 / Biso mean: 39.64 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.21 Å2
2--1.15 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.5→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 96 616 5564
Biso mean--49.5 44.24 -
Num. residues----647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125209
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.6327068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00922.51251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6491530
X-RAY DIFFRACTIONr_chiral_restr0.1030.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024037
X-RAY DIFFRACTIONr_rigid_bond_restr9.4535209
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 442 -
Rwork0.335 7757 -
all-8199 -
obs--96.09 %
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)
10.23720.8044-0.03542.8501-0.06480.07380.4377-0.15810.24351.0047-0.44180.7772-0.12720.0760.00410.5645-0.25870.37720.2036-0.17710.487937.850217.724714.1099
21.42481.3494-0.68221.5653-0.75570.37010.1985-0.04820.07670.0355-0.15950.0292-0.03190.0695-0.03910.2118-0.00870.01970.19840.01920.282438.8415.54235.8867
33.1101-2.28241.91291.6939-1.38941.3014-0.0408-0.1265-0.09870.01140.07270.0037-0.15350.112-0.03190.1868-0.1797-0.11630.38660.14210.375149.0348-4.980118.8698
42.3831-0.20390.33032.1534-2.37652.62940.8607-0.7482-0.20280.6262-0.69450.2009-0.65730.7785-0.16620.5139-0.5023-0.04140.562-0.04930.122948.074216.096622.1518
500000000000000-00.2338000.233800.2338000
60.39430.0644-0.01940.0351-0.12280.6125-0.0162-0.0836-0.0618-0.0048-0.0297-0.0035-0.00930.04970.04590.21390.0048-0.01950.23850.01660.251212.3049-14.052424.8629
70.8006-0.1967-1.64420.76710.10393.5780.4361-0.16220.1532-0.09750.05050.1044-0.87960.3377-0.48670.3318-0.11560.08710.3252-0.01710.240817.66231.420130.4223
80.4765-0.0875-0.04980.0395-0.06640.27390.00730.0270.04990.0115-0.0162-0.02440.0076-0.0160.00890.22450.0047-0.00990.23750.00570.26135.3113-6.694513.1516
90.40180.3786-0.07630.47820.17370.7720.143-0.0065-0.01680.0810.0223-0.0125-0.1268-0.1356-0.16530.25110.02670.03510.29020.02420.2135-6.6093-1.929818.0146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 77
2X-RAY DIFFRACTION2A78 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 247
5X-RAY DIFFRACTION5A248 - 268
6X-RAY DIFFRACTION6B2 - 100
7X-RAY DIFFRACTION7B101 - 196
8X-RAY DIFFRACTION8B197 - 364
9X-RAY DIFFRACTION9B365 - 396

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