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- PDB-9gp0: 4-allyl syringol oxidase from Streptomyces cavernae: complex with... -

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Basic information

Entry
Database: PDB / ID: 9gp0
Title4-allyl syringol oxidase from Streptomyces cavernae: complex with Vanillyl alcohol
Components4-allyl syringol oxidase from Streptomyces cavernae
KeywordsOXIDOREDUCTASE / FAD / flavi / biocatalysis
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / 4-hydroxy-3-methoxybenzaldehyde
Function and homology information
Biological speciesStreptomyces cavernae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)123,8696
Polymers121,9942
Non-polymers1,8754
Water10,052558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-75 kcal/mol
Surface area32700 Å2
Unit cell
Length a, b, c (Å)83.419, 83.419, 298.892
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.06 M of 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-3 / Wavelength: 0.96546 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.75→74.72 Å / Num. obs: 116790 / % possible obs: 99.1 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.048 / Rrim(I) all: 0.118 / Χ2: 1.08 / Net I/σ(I): 8.4 / Num. measured all: 630911
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 98.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 1.371 / Num. measured all: 27255 / Num. unique obs: 5798 / CC1/2: 0.307 / Rpim(I) all: 0.636 / Rrim(I) all: 1.524 / Χ2: 0.84 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→72.24 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.544 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 5790 5 %RANDOM
Rwork0.194 ---
obs0.196 110831 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→72.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8138 0 128 558 8824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138475
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177684
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.64911529
X-RAY DIFFRACTIONr_angle_other_deg1.3891.57717798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21851039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55421.85454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.686151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7191562
X-RAY DIFFRACTIONr_chiral_restr0.0850.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021793
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_it2.3692.9674183
X-RAY DIFFRACTIONr_mcbond_other2.3652.9674182
X-RAY DIFFRACTIONr_mcangle_it3.1874.4425213
X-RAY DIFFRACTIONr_mcangle_other3.1884.4435214
X-RAY DIFFRACTIONr_scbond_it3.3743.3054292
X-RAY DIFFRACTIONr_scbond_other3.3743.3054293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0654.8286317
X-RAY DIFFRACTIONr_long_range_B_refined7.01457.59237878
X-RAY DIFFRACTIONr_long_range_B_other7.00257.55437515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 387 -
Rwork0.35 8228 -
obs--98.81 %

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