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- PDB-9goz: 4-Allyl syringol oxidase from Streptomyces cavernae: complex with... -

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Basic information

Entry
Database: PDB / ID: 9goz
Title4-Allyl syringol oxidase from Streptomyces cavernae: complex with eugenol
Components4-allyl syringol oxidase from Streptomyces cavernae
KeywordsOXIDOREDUCTASE / FAD / flavin / oxygen / biocatalysis
Function / homology2-methoxy-4-(prop-2-en-1-yl)phenol / FLAVIN-ADENINE DINUCLEOTIDE / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces cavernae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMattevi, A. / Alvigini, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Kinetic and structural investigation of the 4-allyl syringol oxidase from Streptomyces cavernae.
Authors: Eggerichs, D. / Weddeling, H.G. / Alvigini, L. / Rapsch, T. / Weindorf, N. / Mattevi, A. / Tischler, D.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-allyl syringol oxidase from Streptomyces cavernae
B: 4-allyl syringol oxidase from Streptomyces cavernae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,81912
Polymers121,9942
Non-polymers2,82510
Water24,8071377
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-50 kcal/mol
Surface area31980 Å2
Unit cell
Length a, b, c (Å)83.259, 83.259, 297.519
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-allyl syringol oxidase from Streptomyces cavernae


Mass: 60996.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cavernae (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 1387 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EOL / 2-methoxy-4-(prop-2-en-1-yl)phenol / eugenol


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1377 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.06 M MgCl2 6 H2O, CaCl2 2 H2O, 0.1 M Tris, bicine, 20% glycerol, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.4→40.89 Å / Num. obs: 228072 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.048 / Rrim(I) all: 0.133 / Χ2: 0.66 / Net I/σ(I): 7.9
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.817 / Num. measured all: 90175 / Num. unique obs: 11284 / CC1/2: 0.672 / Rpim(I) all: 0.307 / Rrim(I) all: 0.873 / Χ2: 0.19 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.521 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 11366 5 %RANDOM
Rwork0.187 ---
obs0.188 216577 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8109 0 192 1377 9678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177736
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.6511561
X-RAY DIFFRACTIONr_angle_other_deg1.5021.58317907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88651044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89621.741448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.269151303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4861562
X-RAY DIFFRACTIONr_chiral_restr0.0890.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021804
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_it1.3891.5524188
X-RAY DIFFRACTIONr_mcbond_other1.3861.5524187
X-RAY DIFFRACTIONr_mcangle_it1.9842.3285228
X-RAY DIFFRACTIONr_mcangle_other1.9852.3285229
X-RAY DIFFRACTIONr_scbond_it2.4351.8034321
X-RAY DIFFRACTIONr_scbond_other2.4341.8044322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6322.6066334
X-RAY DIFFRACTIONr_long_range_B_refined7.17732.08540126
X-RAY DIFFRACTIONr_long_range_B_other6.1130.64238116
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 809 -
Rwork0.33 16104 -
obs--99.92 %

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