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- PDB-8u09: Crystal structure of substrate-free SyoA -

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Basic information

Entry
Database: PDB / ID: 8u09
TitleCrystal structure of substrate-free SyoA
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / O-demethylase / peroxygenase
Function / homologyACETATE ION / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesAmycolatopsis thermoflava N1165 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHarlington, A.C. / Shearwin, K.E. / Bell, S.G. / Whelan, F.
Funding support Australia, 3items
OrganizationGrant numberCountry
Wine AustraliaPH2002 Australia
Australian Research Council (ARC)DP200102411 Australia
Australian Research Council (ARC)DP230103062 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into S-lignin O-demethylation via a rare class of heme peroxygenase enzymes.
Authors: Harlington, A.C. / Das, T. / Shearwin, K.E. / Bell, S.G. / Whelan, F.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 19, 2025Group: Author supporting evidence / Structure summary / Category: audit_author / pdbx_audit_support / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7618
Polymers45,6251
Non-polymers1,1367
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-30 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.860, 150.242, 60.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Cytochrome P450


Mass: 45625.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis thermoflava N1165 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: unspecific monooxygenase
#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-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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, pH 5, 5% w/v gamma-PGA, 12% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 27, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→47.19 Å / Num. obs: 35630 / % possible obs: 98.3 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 19.8
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3483 / CC1/2: 0.939 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→47.19 Å / SU ML: 0.1943 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 1999 5.61 %
Rwork0.1718 33621 -
obs0.1737 35620 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.82 Å2
Refinement stepCycle: LAST / Resolution: 1.98→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 77 293 3440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513312
X-RAY DIFFRACTIONf_angle_d0.84924533
X-RAY DIFFRACTIONf_chiral_restr0.0492480
X-RAY DIFFRACTIONf_plane_restr0.0078597
X-RAY DIFFRACTIONf_dihedral_angle_d8.5901472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.25071390.18722340X-RAY DIFFRACTION98.26
2.03-2.090.25191410.17382356X-RAY DIFFRACTION100
2.09-2.150.23231390.17112351X-RAY DIFFRACTION99.96
2.15-2.220.22551410.16882379X-RAY DIFFRACTION100
2.22-2.30.21381410.16492357X-RAY DIFFRACTION99.96
2.3-2.390.21951410.16662383X-RAY DIFFRACTION99.88
2.39-2.50.18931410.16552378X-RAY DIFFRACTION100
2.5-2.630.21491420.16732393X-RAY DIFFRACTION100
2.63-2.790.21931430.17472386X-RAY DIFFRACTION99.96
2.79-3.010.20191430.18182406X-RAY DIFFRACTION100
3.01-3.310.21681430.17982402X-RAY DIFFRACTION100
3.31-3.790.18721450.16892450X-RAY DIFFRACTION100
3.79-4.780.15581460.15012453X-RAY DIFFRACTION100
4.78-47.190.22331540.19182587X-RAY DIFFRACTION99.78

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