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- PDB-6hqo: Crystal structure of GcoA F169S bound to guaiacol -

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Basic information

Entry
Database: PDB / ID: 6hqo
TitleCrystal structure of GcoA F169S bound to guaiacol
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome / P450 / lignin.
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Guaiacol / Cytochrome P450 / Aromatic O-demethylase, cytochrome P450 subunit
Similarity search - Component
Biological speciesAmycolatopsis sp. ATCC 39116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMallinson, S.J.B. / Hinchen, D.J. / Allen, M.D. / Johnson, C.W. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P011918/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L001926/1 United Kingdom
Department of Energy (DOE, United States)DE-AC36-08GO28308 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Enabling microbial syringol conversion through structure-guided protein engineering.
Authors: Machovina, M.M. / Mallinson, S.J.B. / Knott, B.C. / Meyers, A.W. / Garcia-Borras, M. / Bu, L. / Gado, J.E. / Oliver, A. / Schmidt, G.P. / Hinchen, D.J. / Crowley, M.F. / Johnson, C.W. / ...Authors: Machovina, M.M. / Mallinson, S.J.B. / Knott, B.C. / Meyers, A.W. / Garcia-Borras, M. / Bu, L. / Gado, J.E. / Oliver, A. / Schmidt, G.P. / Hinchen, D.J. / Crowley, M.F. / Johnson, C.W. / Neidle, E.L. / Payne, C.M. / Houk, K.N. / Beckham, G.T. / McGeehan, J.E. / DuBois, J.L.
History
DepositionSep 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9793
Polymers45,2391
Non-polymers7412
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.850, 103.850, 115.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-663-

HOH

21A-1021-

HOH

31A-1048-

HOH

41A-1060-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45238.516 Da / Num. of mol.: 1 / Mutation: F169S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. ATCC 39116 (bacteria)
Gene: AMETH_3834 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076MY51, UniProt: P0DPQ7*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-JZ3 / Guaiacol / 2-methoxyphenol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate, HEPES, guaiacol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→73.43 Å / Num. obs: 69625 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 2 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCB

5ncb


Resolution: 1.7→73.43 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5
RfactorNum. reflection% reflection
Rfree0.1811 3406 4.89 %
Rwork0.1517 --
obs0.1532 69625 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→73.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 52 488 3690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183292
X-RAY DIFFRACTIONf_angle_d1.4564513
X-RAY DIFFRACTIONf_dihedral_angle_d4.651923
X-RAY DIFFRACTIONf_chiral_restr0.106475
X-RAY DIFFRACTIONf_plane_restr0.011597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72430.3151440.26412717X-RAY DIFFRACTION100
1.7243-1.750.28621440.24772724X-RAY DIFFRACTION100
1.75-1.77740.24351230.22382726X-RAY DIFFRACTION100
1.7774-1.80650.22541660.2062687X-RAY DIFFRACTION100
1.8065-1.83770.22731480.19732705X-RAY DIFFRACTION100
1.8377-1.87110.2261450.18242723X-RAY DIFFRACTION100
1.8711-1.90710.22661570.17832706X-RAY DIFFRACTION100
1.9071-1.9460.23411240.16982753X-RAY DIFFRACTION100
1.946-1.98830.18031220.16182756X-RAY DIFFRACTION100
1.9883-2.03460.16351320.14932730X-RAY DIFFRACTION100
2.0346-2.08550.19231410.14132715X-RAY DIFFRACTION100
2.0855-2.14190.1741290.13372756X-RAY DIFFRACTION100
2.1419-2.20490.16491350.13522741X-RAY DIFFRACTION100
2.2049-2.27610.1711530.13682740X-RAY DIFFRACTION100
2.2761-2.35740.16861320.14182758X-RAY DIFFRACTION100
2.3574-2.45180.17771520.15062739X-RAY DIFFRACTION100
2.4518-2.56340.20331430.15942730X-RAY DIFFRACTION100
2.5634-2.69860.21171390.18022786X-RAY DIFFRACTION100
2.6986-2.86760.22061360.17622787X-RAY DIFFRACTION100
2.8676-3.08910.21861460.17122762X-RAY DIFFRACTION100
3.0891-3.39990.17591520.15112791X-RAY DIFFRACTION100
3.3999-3.89190.14381400.12372829X-RAY DIFFRACTION100
3.8919-4.90320.1481620.11372838X-RAY DIFFRACTION100
4.9032-73.50160.15941410.15613020X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.0717 Å / Origin y: 80.3079 Å / Origin z: 42.0367 Å
111213212223313233
T0.2134 Å20.0261 Å2-0.0018 Å2-0.1976 Å2-0.0089 Å2--0.215 Å2
L0.6193 °2-0.0467 °2-0.1031 °2-0.4177 °20.2242 °2--0.6421 °2
S-0.0363 Å °-0.0468 Å °0.0571 Å °0.0686 Å °0.065 Å °-0.0642 Å °0.055 Å °0.0797 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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