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- PDB-6hqn: Crystal structure of GcoA F169L bound to guaiacol -

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Basic information

Entry
Database: PDB / ID: 6hqn
TitleCrystal structure of GcoA F169L 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: 1.87 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)46,0053
Polymers45,2651
Non-polymers7412
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-25 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.000, 104.000, 111.580
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-642-

HOH

21A-1003-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45264.594 Da / Num. of mol.: 1 / Mutation: F169L
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.: 439 / 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: 3.33 Å3/Da / Density % sol: 63.09 %
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: 1.87→76.08 Å / Num. obs: 52238 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 1.87→1.92 Å / Mean I/σ(I) obs: 2.4 / CC1/2: 0.808

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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: 1.87→73.539 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.42
RfactorNum. reflection% reflection
Rfree0.1697 2563 5.01 %
Rwork0.1455 --
obs0.1468 51138 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→73.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 52 439 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133306
X-RAY DIFFRACTIONf_angle_d1.3194533
X-RAY DIFFRACTIONf_dihedral_angle_d4.6021933
X-RAY DIFFRACTIONf_chiral_restr0.082479
X-RAY DIFFRACTIONf_plane_restr0.009599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9060.26761250.24392700X-RAY DIFFRACTION100
1.906-1.94490.23011390.20432622X-RAY DIFFRACTION100
1.9449-1.98720.22511440.18122675X-RAY DIFFRACTION100
1.9872-2.03340.20091370.16742660X-RAY DIFFRACTION100
2.0334-2.08430.21251400.16252647X-RAY DIFFRACTION100
2.0843-2.14070.20171170.15512684X-RAY DIFFRACTION100
2.1407-2.20370.19161460.15382661X-RAY DIFFRACTION100
2.2037-2.27480.20681410.15332675X-RAY DIFFRACTION100
2.2748-2.35610.19521600.15082641X-RAY DIFFRACTION100
2.3561-2.45040.19061520.14792671X-RAY DIFFRACTION100
2.4504-2.5620.19051540.1532660X-RAY DIFFRACTION100
2.562-2.6970.18211500.1712683X-RAY DIFFRACTION100
2.697-2.8660.20631470.16172698X-RAY DIFFRACTION100
2.866-3.08730.18031470.16142695X-RAY DIFFRACTION100
3.0873-3.3980.16131310.14162743X-RAY DIFFRACTION100
3.398-3.88970.13331450.12362744X-RAY DIFFRACTION100
3.8897-4.90050.13131480.11122774X-RAY DIFFRACTION100
4.9005-73.5960.16021400.14792942X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 46.551 Å / Origin y: 80.5115 Å / Origin z: 40.9768 Å
111213212223313233
T0.2485 Å20.0499 Å20.0079 Å2-0.2275 Å20.03 Å2--0.2448 Å2
L0.793 °20.1233 °2-0.2433 °2-0.4338 °20.2224 °2--0.8123 °2
S-0.0609 Å °-0.0739 Å °0.0012 Å °0.1153 Å °0.0428 Å °-0.0652 Å °0.1054 Å °0.1604 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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