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- PDB-8s1j: Crystal structure of t-anethole oxygenase from Stenotrophomonas m... -

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Basic information

Entry
Database: PDB / ID: 8s1j
TitleCrystal structure of t-anethole oxygenase from Stenotrophomonas maltophilia
ComponentsTrans-anethole oxygenase
KeywordsOXIDOREDUCTASE / oxygenase / C=C cleavage / bacterial / heme
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: N Biotechnol / Year: 2024
Title: Discovery of a new class of bacterial heme-containing CC cleaving oxygenases.
Authors: Purwani, N.N. / Rozeboom, H.J. / Willers, V.P. / Wijma, H.J. / Fraaije, M.W.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-anethole oxygenase
B: Trans-anethole oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,07812
Polymers70,2782
Non-polymers1,80010
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, and DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-98 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.254, 96.135, 78.311
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trans-anethole oxygenase


Mass: 35138.992 Da / Num. of mol.: 2 / Mutation: 15 residues truncated from N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M bis-tris propane, 25 % PEG3350
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.83→58.8 Å / Num. obs: 52522 / % possible obs: 91.5 % / Redundancy: 6.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.8
Reflection shellResolution: 1.83→1.94 Å / Rmerge(I) obs: 1.254 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2626 / CC1/2: 0.58 / Rpim(I) all: 0.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→58.8 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.259 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS Completeness ellipsoidal = 91.5 %
RfactorNum. reflection% reflectionSelection details
Rfree0.22782 2630 5 %RANDOM
Rwork0.19177 ---
obs0.19357 49892 82.78 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.09 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.83→58.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 0 119 344 5358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125190
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164812
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.8537076
X-RAY DIFFRACTIONr_angle_other_deg0.561.78311062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.434542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44110834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026236
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021272
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_it1.6522.2262421
X-RAY DIFFRACTIONr_mcbond_other1.6512.2242420
X-RAY DIFFRACTIONr_mcangle_it2.4863.9893028
X-RAY DIFFRACTIONr_mcangle_other2.4863.9913029
X-RAY DIFFRACTIONr_scbond_it2.2312.5242769
X-RAY DIFFRACTIONr_scbond_other2.2312.5242770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5514.544049
X-RAY DIFFRACTIONr_long_range_B_refined4.79523.216145
X-RAY DIFFRACTIONr_long_range_B_other4.75922.366093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å
RfactorNum. reflection% reflection
Rfree0.363 19 -
Rwork0.302 400 -
obs--8.98 %
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)
10.1722-0.0328-0.08190.30410.0460.21050.00620.0066-0.0108-0.02170.006-0.00140.02250.0045-0.01220.0221-0.006-0.00740.02410.00080.018714.594-20.5617.845
20.2487-0.02860.05330.3585-0.02110.22040.0085-0.00460.0124-0.03080.0056-0.0035-0.0196-0.0099-0.01420.0118-0.00230.00390.0092-0.00030.002311.75319.57819.442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 316
2X-RAY DIFFRACTION2B16 - 317

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