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- PDB-8u1i: Crystal structure of SyoA bound to 4-methylsyringol -

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Basic information

Entry
Database: PDB / ID: 8u1i
TitleCrystal structure of SyoA bound to 4-methylsyringol
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / O-demethylase / peroxygenase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / NITRATE ION / :
Function and homology information
Biological speciesAmycolatopsis thermoflava N1165 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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
DepositionSep 1, 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 / Category: pdbx_audit_support

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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)46,5966
Polymers45,6251
Non-polymers9715
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-21 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.414, 62.764, 58.078
Angle α, β, γ (deg.)90.000, 104.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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-UB9 / 2,6-dimethoxy-4-methylphenol


Mass: 168.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.2 M lithium nitrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.12→41.6 Å / Num. obs: 153831 / % possible obs: 99.95 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0695 / Net I/σ(I): 11.41
Reflection shellResolution: 1.12→1.16 Å / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 92855 / CC1/2: 0.626 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8U19

8u19


Resolution: 1.12→41.6 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1535 1993 1.3 %
Rwork0.1374 151369 -
obs0.1376 153362 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.75 Å2
Refinement stepCycle: LAST / Resolution: 1.12→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 67 445 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813490
X-RAY DIFFRACTIONf_angle_d1.13894814
X-RAY DIFFRACTIONf_chiral_restr0.0894513
X-RAY DIFFRACTIONf_plane_restr0.0129645
X-RAY DIFFRACTIONf_dihedral_angle_d7.7073510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.150.25361390.268910378X-RAY DIFFRACTION96.29
1.15-1.180.25961340.227310812X-RAY DIFFRACTION99.97
1.18-1.210.21131500.205810822X-RAY DIFFRACTION99.96
1.21-1.250.19391390.180710765X-RAY DIFFRACTION99.96
1.25-1.30.20821440.164910807X-RAY DIFFRACTION99.96
1.3-1.350.16481420.147910820X-RAY DIFFRACTION99.95
1.35-1.410.16931430.135710805X-RAY DIFFRACTION99.97
1.41-1.480.15711450.123910833X-RAY DIFFRACTION99.97
1.48-1.580.14041430.106410851X-RAY DIFFRACTION99.96
1.58-1.70.14081420.103910820X-RAY DIFFRACTION99.99
1.7-1.870.12951430.111310872X-RAY DIFFRACTION99.99
1.87-2.140.13721410.11910861X-RAY DIFFRACTION100
2.14-2.690.14971440.133410892X-RAY DIFFRACTION99.95
2.69-41.60.14051440.138111031X-RAY DIFFRACTION99.82

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