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- PDB-6hqt: Crystal structure of GcoA F169V bound to syringol -

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Basic information

Entry
Database: PDB / ID: 6hqt
TitleCrystal structure of GcoA F169V 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: 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)46,0213
Polymers45,2511
Non-polymers7712
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-26 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.900, 103.900, 115.580
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-656-

HOH

21A-924-

HOH

31A-950-

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-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.: 392 / 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, 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: 1.85→62 Å / Num. obs: 544478 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 22.5
Reflection shellResolution: 1.85→1.9 Å / Mean I/σ(I) obs: 2.3 / CC1/2: 0.809

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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→50.504 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.91
RfactorNum. reflection% reflection
Rfree0.1788 2722 5 %
Rwork0.1563 --
obs0.1575 54478 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→50.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 54 392 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073304
X-RAY DIFFRACTIONf_angle_d0.94530
X-RAY DIFFRACTIONf_dihedral_angle_d4.511931
X-RAY DIFFRACTIONf_chiral_restr0.053478
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88370.29871340.24282682X-RAY DIFFRACTION100
1.8837-1.91990.22991400.21142689X-RAY DIFFRACTION100
1.9199-1.95910.20391520.1852669X-RAY DIFFRACTION100
1.9591-2.00170.19141300.16642694X-RAY DIFFRACTION100
2.0017-2.04830.19371330.15762693X-RAY DIFFRACTION100
2.0483-2.09950.18061290.1512695X-RAY DIFFRACTION100
2.0995-2.15620.17291620.14342671X-RAY DIFFRACTION100
2.1562-2.21970.19011500.14092696X-RAY DIFFRACTION100
2.2197-2.29130.18411680.152661X-RAY DIFFRACTION100
2.2913-2.37320.16771360.1472699X-RAY DIFFRACTION100
2.3732-2.46830.17441270.15352736X-RAY DIFFRACTION100
2.4683-2.58060.18471570.16712685X-RAY DIFFRACTION100
2.5806-2.71660.21541400.18862719X-RAY DIFFRACTION100
2.7166-2.88680.21291470.18672733X-RAY DIFFRACTION100
2.8868-3.10970.20221410.17612730X-RAY DIFFRACTION100
3.1097-3.42260.17131370.15542759X-RAY DIFFRACTION100
3.4226-3.91760.14431400.12652773X-RAY DIFFRACTION100
3.9176-4.93520.14841490.12542809X-RAY DIFFRACTION100
4.9352-50.52240.17891500.16712963X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.2386 Å / Origin y: 80.3881 Å / Origin z: 42.2287 Å
111213212223313233
T0.218 Å20.0158 Å20.0055 Å2-0.1991 Å2-0.0105 Å2--0.217 Å2
L0.6138 °20.0137 °20.0004 °2-0.3808 °20.1622 °2--0.6042 °2
S-0.0251 Å °-0.052 Å °0.0642 Å °0.0563 Å °0.041 Å °-0.0391 Å °0.0402 Å °0.045 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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