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- PDB-6hqk: Crystal structure of GcoA F169A bound to guaiacol -

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Basic information

Entry
Database: PDB / ID: 6hqk
TitleCrystal structure of GcoA F169A 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: 1.57 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)45,9633
Polymers45,2231
Non-polymers7412
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-25 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.654, 103.654, 114.958
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-686-

HOH

21A-1065-

HOH

31A-1099-

HOH

41A-1101-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45222.516 Da / Num. of mol.: 1 / Mutation: F169A
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.: 529 / 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: 3.41 Å3/Da / Density % sol: 63.97 %
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: 1.57→76.97 Å / Num. obs: 87452 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 1.57→1.61 Å

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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: 1.57→76.97 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1812 4322 4.94 %
Rwork0.1581 --
obs0.1593 87425 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.57→76.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 52 529 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163309
X-RAY DIFFRACTIONf_angle_d1.4554536
X-RAY DIFFRACTIONf_dihedral_angle_d6.1871936
X-RAY DIFFRACTIONf_chiral_restr0.1478
X-RAY DIFFRACTIONf_plane_restr0.011600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5698-1.58760.32081090.28972668X-RAY DIFFRACTION97
1.5876-1.60630.31971240.28072743X-RAY DIFFRACTION100
1.6063-1.62590.29751380.27192712X-RAY DIFFRACTION99
1.6259-1.64650.28141360.25432790X-RAY DIFFRACTION100
1.6465-1.66820.28621360.25192713X-RAY DIFFRACTION100
1.6682-1.6910.23081450.23612728X-RAY DIFFRACTION100
1.691-1.71520.27281520.23562720X-RAY DIFFRACTION100
1.7152-1.74080.2671370.23372731X-RAY DIFFRACTION100
1.7408-1.7680.24851400.21092734X-RAY DIFFRACTION100
1.768-1.7970.23181600.20332737X-RAY DIFFRACTION100
1.797-1.8280.22441390.18852738X-RAY DIFFRACTION100
1.828-1.86120.21651370.17612740X-RAY DIFFRACTION100
1.8612-1.8970.22741370.17532754X-RAY DIFFRACTION100
1.897-1.93570.2011490.1642743X-RAY DIFFRACTION100
1.9357-1.97780.16071460.15542740X-RAY DIFFRACTION100
1.9778-2.02380.19641480.152767X-RAY DIFFRACTION100
2.0238-2.07440.1631610.14722745X-RAY DIFFRACTION100
2.0744-2.13050.17311250.14242778X-RAY DIFFRACTION100
2.1305-2.19320.17471430.13672764X-RAY DIFFRACTION100
2.1932-2.2640.16661510.13942754X-RAY DIFFRACTION100
2.264-2.34490.17011460.14042783X-RAY DIFFRACTION100
2.3449-2.43880.19051490.14012778X-RAY DIFFRACTION100
2.4388-2.54980.15351740.15152761X-RAY DIFFRACTION100
2.5498-2.68430.19961430.16512776X-RAY DIFFRACTION100
2.6843-2.85250.16561450.16892805X-RAY DIFFRACTION100
2.8525-3.07270.17161460.1582814X-RAY DIFFRACTION100
3.0727-3.38190.18241360.14332833X-RAY DIFFRACTION100
3.3819-3.87130.15151470.12012864X-RAY DIFFRACTION100
3.8713-4.87730.12561670.11492857X-RAY DIFFRACTION100
4.8773-77.07420.17611560.16153033X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.0993 Å / Origin y: 80.1351 Å / Origin z: 42.0169 Å
111213212223313233
T0.1215 Å20.0133 Å20.0054 Å2-0.1081 Å2-0.0067 Å2--0.1202 Å2
L0.5127 °2-0.0065 °2-0.048 °2-0.3488 °20.1533 °2--0.5374 °2
S-0.0308 Å °-0.0348 Å °0.0416 Å °0.0454 Å °0.0412 Å °-0.0373 Å °0.0401 Å °0.05 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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