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- PDB-5omu: Crystal structure of Amycolatopsis cytochrome P450 GcoA in comple... -

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Basic information

Entry
Database: PDB / ID: 5omu
TitleCrystal structure of Amycolatopsis cytochrome P450 GcoA in complex with syringol
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / guaiacol / lignin / CYP255A / Amycolatopsis / heme / haem / syringol
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesAmycolatopsis sp. ATCC 39116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMallinson, S.J.B. / Johnson, C.W. / Neidle, E.L. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P0119818/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L001926/1 United Kingdom
Department of Energy (DOE, United States)DE-AC36-08GO28308 United States
CitationJournal: Nat Commun / Year: 2018
Title: A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion.
Authors: Mallinson, S.J.B. / Machovina, M.M. / Silveira, R.L. / Garcia-Borras, M. / Gallup, N. / Johnson, C.W. / Allen, M.D. / Skaf, M.S. / Crowley, M.F. / Neidle, E.L. / Houk, K.N. / Beckham, G.T. / ...Authors: Mallinson, S.J.B. / Machovina, M.M. / Silveira, R.L. / Garcia-Borras, M. / Gallup, N. / Johnson, C.W. / Allen, M.D. / Skaf, M.S. / Crowley, M.F. / Neidle, E.L. / Houk, K.N. / Beckham, G.T. / DuBois, J.L. / McGeehan, J.E.
History
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 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 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)46,2233
Polymers45,4531
Non-polymers7712
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-25 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.360, 105.360, 113.230
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-621-

HOH

21A-1037-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45452.773 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
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.4M sodium malonate, 0.2M syringol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→45.08 Å / Num. obs: 47054 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Net I/σ(I): 26.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3384 / CC1/2: 0.885 / Rpim(I) all: 0.347 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38.567 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.66
RfactorNum. reflection% reflection
Rfree0.1776 2387 5.08 %
Rwork0.1482 --
obs0.1497 46982 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→38.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 54 469 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093310
X-RAY DIFFRACTIONf_angle_d2.234536
X-RAY DIFFRACTIONf_dihedral_angle_d14.8921943
X-RAY DIFFRACTIONf_chiral_restr0.056476
X-RAY DIFFRACTIONf_plane_restr0.007599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98980.28271440.22272575X-RAY DIFFRACTION100
1.9898-2.03310.20131530.18782566X-RAY DIFFRACTION100
2.0331-2.08040.21111170.17612569X-RAY DIFFRACTION100
2.0804-2.13240.19691370.16852597X-RAY DIFFRACTION100
2.1324-2.19010.21081520.15472571X-RAY DIFFRACTION100
2.1901-2.25450.21541280.16022605X-RAY DIFFRACTION100
2.2545-2.32730.16621040.15322610X-RAY DIFFRACTION100
2.3273-2.41040.20061320.15182621X-RAY DIFFRACTION100
2.4104-2.50690.1921490.16382591X-RAY DIFFRACTION100
2.5069-2.6210.25141150.16592624X-RAY DIFFRACTION100
2.621-2.75910.19871570.17462601X-RAY DIFFRACTION100
2.7591-2.93190.20091520.17642604X-RAY DIFFRACTION100
2.9319-3.15820.20651770.18012589X-RAY DIFFRACTION100
3.1582-3.47590.18361640.1482634X-RAY DIFFRACTION100
3.4759-3.97840.1531410.12492660X-RAY DIFFRACTION100
3.9784-5.01060.13391300.11232725X-RAY DIFFRACTION100
5.0106-38.57410.16061350.152853X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.5827 Å / Origin y: 81.4678 Å / Origin z: 41.6036 Å
111213212223313233
T0.3772 Å20.0678 Å20.0123 Å2-0.291 Å20.0242 Å2--0.3497 Å2
L1.629 °20.2886 °2-0.5256 °2-0.8249 °20.1759 °2--1.2253 °2
S-0.1809 Å °-0.1113 Å °0.0383 Å °0.1312 Å °0.1101 Å °-0.0896 Å °0.2144 Å °0.13 Å °0.0592 Å °
Refinement TLS groupSelection details: all

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