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- PDB-6hqm: Crystal structure of GcoA F169I bound to guaiacol -

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Basic information

Entry
Database: PDB / ID: 6hqm
TitleCrystal structure of GcoA F169I 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 / : / 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: 1.85 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)46,1593
Polymers45,4191
Non-polymers7412
Water7,674426
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 area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.210, 105.210, 112.545
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-620-

HOH

21A-995-

HOH

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Components

#1: Protein Cytochrome P450 /


Mass: 45418.762 Da / Num. of mol.: 1 / Mutation: F169I
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 / Heme B


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


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


Mass: 18.015 Da / Num. of mol.: 426 / 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: 64.13 %
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: 1.85→56.25 Å / Num. obs: 54123 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 10.4
Reflection shellResolution: 1.85→1.9 Å / Mean I/σ(I) obs: 2.6 / CC1/2: 0.849

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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: 1.85→52.605 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.6
RfactorNum. reflection% reflection
Rfree0.1799 2649 4.89 %
Rwork0.161 --
obs0.1619 54123 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→52.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 52 426 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093235
X-RAY DIFFRACTIONf_angle_d1.0424439
X-RAY DIFFRACTIONf_dihedral_angle_d4.5391884
X-RAY DIFFRACTIONf_chiral_restr0.06474
X-RAY DIFFRACTIONf_plane_restr0.007581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8503-1.8840.39341330.30392625X-RAY DIFFRACTION98
1.884-1.92020.2941290.28082638X-RAY DIFFRACTION99
1.9202-1.95940.30641500.24652656X-RAY DIFFRACTION99
1.9594-2.0020.2761460.22242627X-RAY DIFFRACTION99
2.002-2.04860.23421350.20842669X-RAY DIFFRACTION99
2.0486-2.09980.22751620.18772646X-RAY DIFFRACTION99
2.0998-2.15660.20271530.17152673X-RAY DIFFRACTION99
2.1566-2.220.18371370.16482670X-RAY DIFFRACTION99
2.22-2.29170.20991290.16562693X-RAY DIFFRACTION99
2.2917-2.37360.18941100.15752708X-RAY DIFFRACTION100
2.3736-2.46860.19351160.15382717X-RAY DIFFRACTION100
2.4686-2.5810.17981520.16452706X-RAY DIFFRACTION100
2.581-2.71710.19861280.17722721X-RAY DIFFRACTION100
2.7171-2.88730.21261270.17782729X-RAY DIFFRACTION100
2.8873-3.11020.16911500.16342737X-RAY DIFFRACTION100
3.1102-3.42310.15991420.14262735X-RAY DIFFRACTION100
3.4231-3.91830.13271330.12752776X-RAY DIFFRACTION100
3.9183-4.93610.13251320.12152819X-RAY DIFFRACTION100
4.9361-52.62620.1681850.16682929X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 46.9146 Å / Origin y: 81.6712 Å / Origin z: 41.3709 Å
111213212223313233
T0.1954 Å20.0441 Å2-0.0019 Å2-0.1769 Å20.0208 Å2--0.1946 Å2
L0.7772 °20.1976 °2-0.1169 °2-0.6199 °20.2588 °2--0.9485 °2
S-0.0226 Å °-0.0623 Å °-0.0147 Å °0.1149 Å °0.0252 Å °-0.0265 Å °0.0924 Å °0.1274 Å °-0.0055 Å °
Refinement TLS groupSelection details: all

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