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- PDB-8eh1: Engineered tyrosine synthase (TmTyrS1) derived from T. maritima T... -

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Basic information

Entry
Database: PDB / ID: 8eh1
TitleEngineered tyrosine synthase (TmTyrS1) derived from T. maritima TrpB with Ser bound as the amino-acrylate intermediate and complexed with 4-hydroxyquinoline
ComponentsEngineered tyrosine synthase (TmTyrS1)
KeywordsBIOSYNTHETIC PROTEIN / tyrosine synthase / engineered enzyme / noncanonical amino acid synthase
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-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
Chem-0JO / quinolin-4-ol / : / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: 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.
#3: 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.
#4: 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

Downloads & links

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Assembly

Deposited unit
A: Engineered tyrosine synthase (TmTyrS1)
B: Engineered tyrosine synthase (TmTyrS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4048
Polymers87,4042
Non-polymers1,0016
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-13 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.862, 164.862, 84.057
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

#1: Protein Engineered tyrosine synthase (TmTyrS1)


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
#2: 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.: 2 / Source method: obtained synthetically / Formula: C11H13N2O7P
#3: Chemical ChemComp-ES1 / quinolin-4-ol


Mass: 145.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
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: 3.27 Å3/Da / Density % sol: 62.35 %
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), 0.2 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: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→38.86 Å / Num. obs: 75913 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 38.89 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.03 / Net I/σ(I): 15.9
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 1.73 / Num. unique obs: 61692 / CC1/2: 0.69 / Rpim(I) all: 0.48

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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→38.86 Å / SU ML: 0.2393 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 3846 5.07 %
Rwork0.1878 72053 -
obs0.1893 75899 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.07 Å2
Refinement stepCycle: LAST / Resolution: 2→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5786 0 66 172 6024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625992
X-RAY DIFFRACTIONf_angle_d0.74718135
X-RAY DIFFRACTIONf_chiral_restr0.0451895
X-RAY DIFFRACTIONf_plane_restr0.0051054
X-RAY DIFFRACTIONf_dihedral_angle_d14.97142145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.33771500.26782647X-RAY DIFFRACTION99.96
2.03-2.050.29751110.26092693X-RAY DIFFRACTION99.86
2.05-2.080.33841480.26042654X-RAY DIFFRACTION100
2.08-2.110.27081360.2492653X-RAY DIFFRACTION99.86
2.11-2.140.28941520.24422670X-RAY DIFFRACTION100
2.14-2.170.32471160.24452665X-RAY DIFFRACTION98.86
2.17-2.210.26961590.23932628X-RAY DIFFRACTION99.79
2.21-2.250.27371600.21892644X-RAY DIFFRACTION99.89
2.25-2.290.24981640.21612669X-RAY DIFFRACTION99.96
2.29-2.330.26461470.21592638X-RAY DIFFRACTION99.93
2.33-2.380.2611410.21762642X-RAY DIFFRACTION99.86
2.38-2.430.27531370.21082687X-RAY DIFFRACTION99.96
2.43-2.490.20751540.20612639X-RAY DIFFRACTION99.93
2.49-2.550.23441470.20512655X-RAY DIFFRACTION100
2.55-2.620.22021530.19852659X-RAY DIFFRACTION99.86
2.62-2.70.2421350.20292686X-RAY DIFFRACTION99.93
2.7-2.780.23011430.20832616X-RAY DIFFRACTION99
2.78-2.880.26441360.20822691X-RAY DIFFRACTION99.37
2.88-30.22991460.19972675X-RAY DIFFRACTION100
3-3.140.27821430.20692656X-RAY DIFFRACTION99.93
3.14-3.30.2141460.20162695X-RAY DIFFRACTION100
3.3-3.510.24681200.19222699X-RAY DIFFRACTION100
3.51-3.780.21391260.16982697X-RAY DIFFRACTION100
3.78-4.160.17431300.16572659X-RAY DIFFRACTION98.87
4.16-4.760.17621450.14442708X-RAY DIFFRACTION100
4.76-5.990.17871660.16422686X-RAY DIFFRACTION100
5.99-38.860.18461350.17152742X-RAY DIFFRACTION98.46

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