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

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Basic information

Entry
Database: PDB / ID: 5ncb
TitleCrystal structure of Amycolatopsis cytochrome P450 GcoA in complex with guaiacol.
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / guaiacol / lignin / CYP255A / Amycolatopsis / heme / haem
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 / Guaiacol / Cytochrome P450
Similarity search - Component
Biological speciesAmycolatopsis sp. ATCC 39116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 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
DepositionMar 3, 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 / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)46,5693
Polymers45,8281
Non-polymers7412
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
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)104.080, 104.080, 115.754
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-892-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45827.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. ATCC 39116 (bacteria)
Gene: WP_020419855 / 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-JZ3 / Guaiacol / 2-methoxyphenol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 279 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: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.44→115.75 Å / Num. obs: 114601 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.024 / Net I/σ(I): 21
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5611 / CC1/2: 0.794 / Rpim(I) all: 0.333 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→77.39 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.773 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15141 5812 5.1 %RANDOM
Rwork0.12773 ---
obs0.12892 108389 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.622 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.44→77.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 52 303 3519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193357
X-RAY DIFFRACTIONr_bond_other_d0.0020.022991
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9774606
X-RAY DIFFRACTIONr_angle_other_deg1.07636918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37723.558163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1815472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3991527
X-RAY DIFFRACTIONr_chiral_restr0.160.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213824
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02719
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5792.1471631
X-RAY DIFFRACTIONr_mcbond_other1.5682.1441630
X-RAY DIFFRACTIONr_mcangle_it2.0083.2292041
X-RAY DIFFRACTIONr_mcangle_other2.0093.2312042
X-RAY DIFFRACTIONr_scbond_it2.7022.4781726
X-RAY DIFFRACTIONr_scbond_other2.7012.4781727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2023.6132565
X-RAY DIFFRACTIONr_long_range_B_refined3.2426.4883888
X-RAY DIFFRACTIONr_long_range_B_other3.07226.143826
X-RAY DIFFRACTIONr_rigid_bond_restr2.74336347
X-RAY DIFFRACTIONr_sphericity_free20.8275202
X-RAY DIFFRACTIONr_sphericity_bonded9.7956348
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 461 -
Rwork0.228 7894 -
obs--99.79 %

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