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- PDB-6hqs: Crystal structure of GcoA F169S bound to syringol -

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Basic information

Entry
Database: PDB / ID: 6hqs
TitleCrystal structure of GcoA F169S bound to syringol
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
2,6-dimethoxyphenol / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 / Aromatic O-demethylase, cytochrome P450 subunit
Similarity search - Component
Biological speciesAmycolatopsis sp. ATCC 39116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0093
Polymers45,2391
Non-polymers7712
Water4,234235
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 area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.291, 104.291, 114.035
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-611-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45238.516 Da / Num. of mol.: 1
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-3DM / 2,6-dimethoxyphenol


Mass: 154.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 64.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate, HEPES, syringol.

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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: 2.17→61.91 Å / Num. obs: 33716 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 20.9
Reflection shellResolution: 2.17→2.23 Å / Mean I/σ(I) obs: 3 / CC1/2: 0.865

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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: 2.17→52.145 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.5
RfactorNum. reflection% reflection
Rfree0.1858 1637 4.86 %
Rwork0.1608 --
obs0.162 33716 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.17→52.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 54 235 3411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083272
X-RAY DIFFRACTIONf_angle_d0.9384488
X-RAY DIFFRACTIONf_dihedral_angle_d4.4431908
X-RAY DIFFRACTIONf_chiral_restr0.051475
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1704-2.23420.29321460.25072572X-RAY DIFFRACTION98
2.2342-2.30630.27081350.23582629X-RAY DIFFRACTION99
2.3063-2.38880.26491180.21052621X-RAY DIFFRACTION99
2.3888-2.48440.23971160.19932666X-RAY DIFFRACTION99
2.4844-2.59750.20861450.19222599X-RAY DIFFRACTION99
2.5975-2.73440.22211400.19992648X-RAY DIFFRACTION100
2.7344-2.90570.19991430.19032648X-RAY DIFFRACTION100
2.9057-3.13010.25311220.17342673X-RAY DIFFRACTION100
3.1301-3.4450.17031560.14872673X-RAY DIFFRACTION100
3.445-3.94330.16611250.1262712X-RAY DIFFRACTION100
3.9433-4.96760.12551530.11762739X-RAY DIFFRACTION100
4.9676-52.16050.17181380.16072899X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 46.8174 Å / Origin y: 80.8346 Å / Origin z: 41.6802 Å
111213212223313233
T0.2917 Å20.0571 Å2-0.0134 Å2-0.2309 Å20.0446 Å2--0.2653 Å2
L0.7771 °20.3188 °2-0.0182 °2-0.5737 °20.4947 °2--0.8917 °2
S0.0032 Å °-0.0378 Å °0.0021 Å °0.183 Å °0.0067 Å °-0.0483 Å °0.096 Å °0.1325 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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