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

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Basic information

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


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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 / 4-hydroxy-3-methoxybenzaldehyde / Cytochrome P450
Similarity search - Component
Biological speciesAmycolatopsis sp. ATCC 39116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMallinson, S.J.B. / Johnson, C.W. / Neidle, E.L. / Beckham, G.T. / McGeehan, J.E.
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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GcoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2213
Polymers45,4531
Non-polymers7692
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-23 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.110, 104.110, 115.660
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-663-

HOH

21A-1057-

HOH

31A-1086-

HOH

41A-1090-

HOH

51A-1126-

HOH

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Components

#1: Protein GcoA / 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)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEE9*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-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 64.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.4M Sodium Malonate pH 7.0; 0.2M vanillin (in DMSO).

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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: 1.68→47.47 Å / Num. obs: 72850 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Net I/σ(I): 22.7
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 5308 / CC1/2: 0.921 / Rpim(I) all: 0.284 / % 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
Starting model: 5NCB

5ncb


Resolution: 1.68→36.808 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1695 3596 4.94 %
Rwork0.1474 --
obs0.1485 72761 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→36.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 54 553 3774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013394
X-RAY DIFFRACTIONf_angle_d2.244662
X-RAY DIFFRACTIONf_dihedral_angle_d4.6052735
X-RAY DIFFRACTIONf_chiral_restr0.061487
X-RAY DIFFRACTIONf_plane_restr0.008613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70210.23891300.21862643X-RAY DIFFRACTION100
1.7021-1.72540.24381430.1882600X-RAY DIFFRACTION100
1.7254-1.75010.17831420.1722625X-RAY DIFFRACTION100
1.7501-1.77620.19231330.16752605X-RAY DIFFRACTION100
1.7762-1.8040.17041400.15892629X-RAY DIFFRACTION100
1.804-1.83350.20311190.15822649X-RAY DIFFRACTION100
1.8335-1.86510.18321440.15752609X-RAY DIFFRACTION100
1.8651-1.89910.18041300.15572637X-RAY DIFFRACTION100
1.8991-1.93560.17871350.15532626X-RAY DIFFRACTION100
1.9356-1.97510.18521210.15732637X-RAY DIFFRACTION100
1.9751-2.0180.16091420.14532647X-RAY DIFFRACTION100
2.018-2.0650.19391550.14712600X-RAY DIFFRACTION100
2.065-2.11660.19051480.14262620X-RAY DIFFRACTION100
2.1166-2.17380.16631190.14052665X-RAY DIFFRACTION100
2.1738-2.23780.15241370.13742639X-RAY DIFFRACTION100
2.2378-2.310.15651600.14462647X-RAY DIFFRACTION100
2.31-2.39260.15121300.1432642X-RAY DIFFRACTION100
2.3926-2.48830.16191530.15652645X-RAY DIFFRACTION100
2.4883-2.60150.17731300.15922683X-RAY DIFFRACTION100
2.6015-2.73870.19321370.17272675X-RAY DIFFRACTION100
2.7387-2.91020.1961320.17622665X-RAY DIFFRACTION100
2.9102-3.13480.18411590.16082678X-RAY DIFFRACTION100
3.1348-3.450.15571440.13882691X-RAY DIFFRACTION100
3.45-3.94870.14781370.11542722X-RAY DIFFRACTION100
3.9487-4.97310.13831320.11642779X-RAY DIFFRACTION100
4.9731-36.81730.17451440.15962907X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.2549 Å / Origin y: 80.4021 Å / Origin z: 42.1472 Å
111213212223313233
T0.1639 Å20.0184 Å20.0056 Å2-0.1521 Å2-0.0145 Å2--0.168 Å2
L0.7183 °20.0126 °2-0.001 °2-0.4928 °20.1452 °2--0.619 °2
S-0.03 Å °-0.0711 Å °0.0698 Å °0.0687 Å °0.0475 Å °-0.0572 Å °0.0283 Å °0.0465 Å °-0.0168 Å °
Refinement TLS groupSelection details: all

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