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

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Basic information

Entry
Database: PDB / ID: 9gov
Title4-Allyl syringol oxidase from Streptomyces cavernae: complex with Propanol syringol
Components4-Allyl syringol oxidase from Streptomyces cavernae
KeywordsOXIDOREDUCTASE / flavin / oxidase / biocatalysis / FAD
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / 2,6-dimethoxy-4-(3-oxidanylpropyl)phenol
Function and homology information
Biological speciesStreptomyces cavernae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlvigini, L. / Mattevi, A.
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)123,9906
Polymers121,9942
Non-polymers1,9964
Water10,377576
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-78 kcal/mol
Surface area32910 Å2
Unit cell
Length a, b, c (Å)82.993, 82.993, 297.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#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)
#2: Chemical ChemComp-QBF / 2,6-dimethoxy-4-(3-oxidanylpropyl)phenol / propanol syringol


Mass: 212.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.06 M of MgCl26 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: SLS / Beamline: X06DA / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2→45.88 Å / Num. obs: 77465 / % possible obs: 99.4 % / Redundancy: 4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.053 / Rrim(I) all: 0.107 / Χ2: 1.05 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.04 Å / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.81 / Num. measured all: 18567 / Num. unique obs: 4585 / CC1/2: 0.524 / Rpim(I) all: 0.459 / Rrim(I) all: 0.933 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.924 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22921 3915 5.1 %RANDOM
Rwork0.18362 ---
obs0.18589 73450 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.887 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å2-0 Å2
2---0.23 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 2→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8127 0 136 576 8839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177643
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6511428
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5817700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65651026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75721.871449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9541561
X-RAY DIFFRACTIONr_chiral_restr0.0790.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029467
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021771
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_it2.9813.6534143
X-RAY DIFFRACTIONr_mcbond_other2.983.6534142
X-RAY DIFFRACTIONr_mcangle_it4.0785.4645156
X-RAY DIFFRACTIONr_mcangle_other4.0785.4645157
X-RAY DIFFRACTIONr_scbond_it3.4583.9824265
X-RAY DIFFRACTIONr_scbond_other3.4583.9834266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1185.8466273
X-RAY DIFFRACTIONr_long_range_B_refined8.11770.32737473
X-RAY DIFFRACTIONr_long_range_B_other8.10870.31237057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 296 -
Rwork0.284 5445 -
obs--99.97 %

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