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- PDB-8r2s: Heme-dependent l-tyrosine hydroxylase (TyrH) from Streptomyces sc... -

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Basic information

Entry
Database: PDB / ID: 8r2s
TitleHeme-dependent l-tyrosine hydroxylase (TyrH) from Streptomyces sclerotialus: fourfold mutant
ComponentsL-tyrosine 3-hydroxylase
KeywordsOXIDOREDUCTASE / Heme / peroxidase / peroxygenase
Function / homologyACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / INDOLE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCarraretto, D. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission824017 B-ligzymesEuropean Union
CitationJournal: Chemcatchem / Year: 2024
Title: Broadening the Catalytic Scope of the Peroxygenase Activity of a Bacterial Tyrosine Hydroxylase
Authors: Carraretto, D. / Alonso-Cotchico, L. / Martin, C. / Trajkovic, M. / van Beek, H.L. / Mattevi, A. / Fraaije, M.W. / Lucas, M.F. / Loncar, N.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-tyrosine 3-hydroxylase
B: L-tyrosine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,20312
Polymers68,6682
Non-polymers1,53610
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint9 kcal/mol
Surface area24330 Å2
Unit cell
Length a, b, c (Å)51.610, 74.834, 156.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein L-tyrosine 3-hydroxylase / Heme-dependent l-tyrosine hydroxylase (TyrH)


Mass: 34333.797 Da / Num. of mol.: 2 / Mutation: S76E, Y141M, M203L, R271A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sclerotialus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): Neb10beta
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 1 M imidazole/Mes monohydrate, 0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 sodium citrate tribasic dihydrate, 0.2 M sodium potassium tartrate tetrahydrate, 0.2 M sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.7→156.91 Å / Num. obs: 17405 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.087 / Rrim(I) all: 0.221 / Χ2: 1.01 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.799 / Num. measured all: 14381 / Num. unique obs: 2266 / CC1/2: 0.765 / Rpim(I) all: 0.345 / Rrim(I) all: 0.872 / Χ2: 1.09 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→78.45 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.866 / SU B: 13.68 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28663 868 5 %RANDOM
Rwork0.20755 ---
obs0.21132 16491 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0 Å2
2---1.15 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.7→78.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 105 0 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134462
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174203
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6656065
X-RAY DIFFRACTIONr_angle_other_deg1.2631.589659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6445541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77920.29241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00415679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8961543
X-RAY DIFFRACTIONr_chiral_restr0.070.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025002
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021038
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.654.0752180
X-RAY DIFFRACTIONr_mcbond_other3.6484.0742179
X-RAY DIFFRACTIONr_mcangle_it5.6086.0972715
X-RAY DIFFRACTIONr_mcangle_other5.6076.0992716
X-RAY DIFFRACTIONr_scbond_it3.7864.4432282
X-RAY DIFFRACTIONr_scbond_other3.7854.4422283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8856.5683351
X-RAY DIFFRACTIONr_long_range_B_refined9.01448.7114984
X-RAY DIFFRACTIONr_long_range_B_other9.01348.714985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 60 -
Rwork0.284 1202 -
obs--100 %

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