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- PDB-8vwk: Crystal Structure of a fatty acid decarboxylase from Kocuria mari... -

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Basic information

Entry
Database: PDB / ID: 8vwk
TitleCrystal Structure of a fatty acid decarboxylase from Kocuria marina in complex with myristic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450
Function / homology
Function and homology information


sterol metabolic 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, E-class, group I / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MYRISTIC ACID / DI(HYDROXYETHYL)ETHER / Cytochrome P450
Similarity search - Component
Biological speciesKocuria marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGeneroso, W.C. / Miyamoto, R.Y. / Murakami, M.T. / Zanphorlin, L.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/02865-2 Brazil
Sao Paulo Research Foundation (FAPESP)2019/08855-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/14410-2 Brazil
CitationJournal: Nat Commun / Year: 2025
Title: Coordinated conformational changes in P450 decarboxylases enable hydrocarbons production from renewable feedstocks.
Authors: Generoso, W.C. / Alvarenga, A.H.S. / Simoes, I.T. / Miyamoto, R.Y. / Melo, R.R. / Guilherme, E.P.X. / Mandelli, F. / Santos, C.A. / Prata, R. / Santos, C.R.D. / Colombari, F.M. / Morais, M.A. ...Authors: Generoso, W.C. / Alvarenga, A.H.S. / Simoes, I.T. / Miyamoto, R.Y. / Melo, R.R. / Guilherme, E.P.X. / Mandelli, F. / Santos, C.A. / Prata, R. / Santos, C.R.D. / Colombari, F.M. / Morais, M.A.B. / Pimentel Fernandes, R. / Persinoti, G.F. / Murakami, M.T. / Zanphorlin, L.M.
History
DepositionFeb 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)50,8949
Polymers49,4831
Non-polymers1,4118
Water2,486138
1
A: Cytochrome P450
hetero molecules

A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,78918
Polymers98,9662
Non-polymers2,82316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)88.722, 88.722, 117.975
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450


Mass: 49482.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kocuria marina (bacteria) / Gene: AS25_12605 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B0D9P4

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10 % w/v PEG400, 4 M NaCl and 0.1 M Hepes (pH 7.5). The protein was concentrated to 60 mg/mL in 100 mM potassium phosphate, 5 % (w/v) glycerol, 150 mM NaCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.05→46.79 Å / Num. obs: 34276 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 55.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.1 / Net I/σ(I): 18.07
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.05-2.172.96754610.4553.0461
2.17-2.321.61851190.7241.661
2.32-2.510.85847930.920.8791
2.51-2.750.45744380.9780.4681
2.75-3.070.22540280.9940.231
3.07-3.540.10535760.9990.1081
3.54-4.330.05930410.9990.061
4.33-6.10.05124000.9990.0521
6.1-46.790.042142010.0431

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.79 Å / SU ML: 0.3253 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1714 5 %
Rwork0.2016 32559 -
obs0.2028 34273 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.26 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 96 138 3564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313502
X-RAY DIFFRACTIONf_angle_d0.62734745
X-RAY DIFFRACTIONf_chiral_restr0.0404501
X-RAY DIFFRACTIONf_plane_restr0.0051622
X-RAY DIFFRACTIONf_dihedral_angle_d12.39111291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.35961400.33952671X-RAY DIFFRACTION99.79
2.11-2.180.33861400.30282659X-RAY DIFFRACTION100
2.18-2.260.35811410.29692668X-RAY DIFFRACTION100
2.26-2.350.3141410.28412692X-RAY DIFFRACTION100
2.35-2.450.30461430.25522705X-RAY DIFFRACTION100
2.45-2.580.27991410.24242678X-RAY DIFFRACTION99.96
2.58-2.740.2661410.23972688X-RAY DIFFRACTION100
2.74-2.960.28651430.25832719X-RAY DIFFRACTION100
2.96-3.250.27721420.2462693X-RAY DIFFRACTION100
3.25-3.720.23121450.20792744X-RAY DIFFRACTION100
3.72-4.690.16791450.15612762X-RAY DIFFRACTION100
4.69-46.790.19191520.16312880X-RAY DIFFRACTION99.87

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