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- PDB-8u19: Crystal structure of SyoA bound to syringol -

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Basic information

Entry
Database: PDB / ID: 8u19
TitleCrystal structure of SyoA bound to syringol
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / o-demethylase / peroxygenase
Function / homology2,6-dimethoxyphenol / PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION
Function and homology information
Biological speciesAmycolatopsis thermoflava N1165 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 31, 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)46,6688
Polymers45,6251
Non-polymers1,0437
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-22 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.851, 62.353, 58.710
Angle α, β, γ (deg.)90.000, 103.060, 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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 521 molecules

#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-3DM / 2,6-dimethoxyphenol


Mass: 154.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O3
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M magnesium nitrate hexahydrate, 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: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 15, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.26→42.15 Å / Num. obs: 108149 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.72
Reflection shellResolution: 1.261→1.306 Å / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 10185 / CC1/2: 0.818 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8U09

8u09


Resolution: 1.26→42.15 Å / SU ML: 0.1155 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.2386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1819 2005 1.86 %
Rwork0.1463 105883 -
obs0.1469 107888 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.26→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 71 514 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643522
X-RAY DIFFRACTIONf_angle_d1.05534865
X-RAY DIFFRACTIONf_chiral_restr0.085521
X-RAY DIFFRACTIONf_plane_restr0.0114653
X-RAY DIFFRACTIONf_dihedral_angle_d7.609519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.36211330.3066969X-RAY DIFFRACTION91.17
1.29-1.330.28551370.24247634X-RAY DIFFRACTION99.77
1.33-1.370.1731530.16797594X-RAY DIFFRACTION99.64
1.37-1.410.20771420.15727593X-RAY DIFFRACTION99.59
1.41-1.460.17421420.14687581X-RAY DIFFRACTION99.61
1.46-1.520.15321470.13257597X-RAY DIFFRACTION99.27
1.52-1.590.16011430.11777573X-RAY DIFFRACTION99.29
1.59-1.670.14981410.11397586X-RAY DIFFRACTION99.18
1.67-1.780.14681420.12187662X-RAY DIFFRACTION99.94
1.78-1.920.20931450.16057549X-RAY DIFFRACTION98.79
1.92-2.110.19211430.14417608X-RAY DIFFRACTION99.27
2.11-2.410.18851430.15297531X-RAY DIFFRACTION97.85
2.41-3.040.18081450.14747594X-RAY DIFFRACTION98.51
3.04-42.150.16861490.1367812X-RAY DIFFRACTION99.94

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