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- PDB-8egy: Engineered holo tyrosine synthase (TmTyrS1) derived from T. marit... -

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Basic information

Entry
Database: PDB / ID: 8egy
TitleEngineered holo tyrosine synthase (TmTyrS1) derived from T. maritima TrpB
ComponentsTryptophan synthase beta chain 1
KeywordsBIOSYNTHETIC PROTEIN / tyrosine synthase / engineered enzyme / noncanonical amino acid synthase
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPorter, N.J. / Almhjell, P.J. / Arnold, F.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125887 United States
Citation
Journal: Nat.Chem.Biol. / Year: 2024
Title: The beta-subunit of tryptophan synthase is a latent tyrosine synthase.
Authors: Almhjell, P.J. / Johnston, K.E. / Porter, N.J. / Kennemur, J.L. / Bhethanabotla, V.C. / Ducharme, J. / Arnold, F.H.
#1: Journal: J Appl Crystallogr / Year: 2007
Title: Phaser crystallographic software.
Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: XDS.
Authors: Kabsch, W.
History
DepositionSep 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,35211
Polymers87,4042
Non-polymers9499
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-22 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.606, 164.606, 83.139
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan synthase beta chain 1


Mass: 43701.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered from tryptophan synthase beta chain 1 / Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: trpB1, trpB, TM_0138 / Production host: Escherichia coli (E. coli) / References: UniProt: P50909, tryptophan synthase

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Non-polymers , 5 types, 227 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsThe starting construct was tryptophan synthase beta chain 1, which was engineered to produce the ...The starting construct was tryptophan synthase beta chain 1, which was engineered to produce the construct used for expression and crystallization.

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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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.2 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic, 0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), 0.1 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→39.15 Å / Num. obs: 69702 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 45.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Net I/σ(I): 21
Reflection shellResolution: 2.05→2.08 Å / Rmerge(I) obs: 2.017 / Num. unique obs: 4504 / CC1/2: 0.622 / Rpim(I) all: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVZ

5dvz


Resolution: 2.05→38.8 Å / SU ML: 0.3033 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 3488 5.01 %
Rwork0.2163 66190 -
obs0.2171 69678 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.92 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5933 0 24 218 6175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196099
X-RAY DIFFRACTIONf_angle_d0.46988251
X-RAY DIFFRACTIONf_chiral_restr0.0415896
X-RAY DIFFRACTIONf_plane_restr0.00321063
X-RAY DIFFRACTIONf_dihedral_angle_d7.7125866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.39921300.36342646X-RAY DIFFRACTION99.89
2.08-2.110.38191550.33312644X-RAY DIFFRACTION99.93
2.11-2.140.29411600.31512599X-RAY DIFFRACTION100
2.14-2.170.35731480.30922607X-RAY DIFFRACTION99.89
2.17-2.210.30461080.30592667X-RAY DIFFRACTION100
2.21-2.250.30781400.29362692X-RAY DIFFRACTION100
2.25-2.290.30331240.28752597X-RAY DIFFRACTION100
2.29-2.330.32661430.27982655X-RAY DIFFRACTION99.93
2.33-2.380.3111530.2822603X-RAY DIFFRACTION100
2.38-2.430.29741250.27912666X-RAY DIFFRACTION100
2.43-2.490.29621110.27942653X-RAY DIFFRACTION100
2.49-2.550.32131490.27122602X-RAY DIFFRACTION100
2.55-2.620.3081470.26132666X-RAY DIFFRACTION99.93
2.62-2.70.27231260.25832645X-RAY DIFFRACTION99.93
2.7-2.780.26451740.2492606X-RAY DIFFRACTION99.89
2.78-2.880.28461090.25662696X-RAY DIFFRACTION100
2.88-30.2911570.25492623X-RAY DIFFRACTION100
3-3.130.27151070.25112652X-RAY DIFFRACTION99.96
3.13-3.30.25221400.23952663X-RAY DIFFRACTION99.96
3.3-3.50.21121440.21872656X-RAY DIFFRACTION100
3.5-3.780.22011300.19372663X-RAY DIFFRACTION99.64
3.78-4.150.20391570.18482637X-RAY DIFFRACTION100
4.16-4.750.16381550.16142666X-RAY DIFFRACTION99.72
4.76-5.980.1811470.17222659X-RAY DIFFRACTION99.96
5.99-38.80.20191490.17442727X-RAY DIFFRACTION99.45

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