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- PDB-6hqp: Crystal structure of GcoA F169V bound to guaiacol -

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Basic information

Entry
Database: PDB / ID: 6hqp
TitleCrystal structure of GcoA F169V 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: 1.62 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)45,9913
Polymers45,2511
Non-polymers7412
Water8,755486
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 area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.803, 103.803, 115.778
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-653-

HOH

21A-999-

HOH

31A-1041-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45250.566 Da / Num. of mol.: 1 / Mutation: F169V
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.: 486 / 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: 3.45 Å3/Da / Density % sol: 64.31 %
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: 1.62→73.4 Å / Num. obs: 80413 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.62→1.66 Å / Mean I/σ(I) obs: 2.1 / CC1/2: 0.828

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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: 1.62→73.4 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.75
RfactorNum. reflection% reflection
Rfree0.1874 4066 5.06 %
Rwork0.1649 --
obs0.1661 80413 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→73.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 52 486 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163302
X-RAY DIFFRACTIONf_angle_d1.3684527
X-RAY DIFFRACTIONf_dihedral_angle_d6.1841931
X-RAY DIFFRACTIONf_chiral_restr0.09478
X-RAY DIFFRACTIONf_plane_restr0.01598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6201-1.63910.36021400.33772562X-RAY DIFFRACTION99
1.6391-1.65910.34411290.31452579X-RAY DIFFRACTION99
1.6591-1.68010.32461420.3052582X-RAY DIFFRACTION99
1.6801-1.70220.31091380.28972590X-RAY DIFFRACTION99
1.7022-1.72550.28791580.26582581X-RAY DIFFRACTION100
1.7255-1.75020.31681330.24932578X-RAY DIFFRACTION99
1.7502-1.77630.24381370.23922586X-RAY DIFFRACTION99
1.7763-1.80410.25461450.22112597X-RAY DIFFRACTION99
1.8041-1.83370.22471370.21122608X-RAY DIFFRACTION100
1.8337-1.86530.21071390.19762587X-RAY DIFFRACTION100
1.8653-1.89920.23451530.19382587X-RAY DIFFRACTION100
1.8992-1.93570.23261270.18682622X-RAY DIFFRACTION100
1.9357-1.97520.19561340.18322598X-RAY DIFFRACTION100
1.9752-2.01820.20581360.17112641X-RAY DIFFRACTION100
2.0182-2.06510.20531350.15822607X-RAY DIFFRACTION100
2.0651-2.11680.1841240.15472657X-RAY DIFFRACTION100
2.1168-2.1740.2181330.14872616X-RAY DIFFRACTION100
2.174-2.2380.18831290.14452625X-RAY DIFFRACTION100
2.238-2.31020.15851520.14312651X-RAY DIFFRACTION100
2.3102-2.39280.17331510.14342607X-RAY DIFFRACTION100
2.3928-2.48860.19121430.15422636X-RAY DIFFRACTION100
2.4886-2.60190.1781590.15852629X-RAY DIFFRACTION100
2.6019-2.73910.21221230.17742666X-RAY DIFFRACTION100
2.7391-2.91070.19831530.17362643X-RAY DIFFRACTION100
2.9107-3.13540.18821430.16162689X-RAY DIFFRACTION100
3.1354-3.4510.16841240.14672697X-RAY DIFFRACTION100
3.451-3.95030.1271640.12392675X-RAY DIFFRACTION100
3.9503-4.97680.12741460.12012751X-RAY DIFFRACTION100
4.9768-73.47520.18811390.16992900X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.0724 Å / Origin y: 80.1826 Å / Origin z: 42.2602 Å
111213212223313233
T0.1393 Å20.0141 Å20.0058 Å2-0.1321 Å2-0.0209 Å2--0.1425 Å2
L0.6229 °2-0.0837 °2-0.0417 °2-0.4191 °20.1592 °2--0.528 °2
S-0.0383 Å °-0.0597 Å °0.0815 Å °0.0485 Å °0.0633 Å °-0.0621 Å °0.0376 Å °0.036 Å °0.0022 Å °
Refinement TLS groupSelection details: all

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