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- PDB-8w1k: Crystal Structure of a fatty acid decarboxylase from Corynebacter... -

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Basic information

Entry
Database: PDB / ID: 8w1k
TitleCrystal Structure of a fatty acid decarboxylase from Corynebacterium lipophiloflavum in complex with oleic acid
ComponentsFatty acid decarboxylase
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 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OLEIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Unspecific monooxygenase
Similarity search - Component
Biological speciesCorynebacterium lipophiloflavum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 16, 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
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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid decarboxylase
B: Fatty acid decarboxylase
C: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,11922
Polymers148,1803
Non-polymers3,93919
Water18,3031016
1
A: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8609
Polymers49,3931
Non-polymers1,4678
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7337
Polymers49,3931
Non-polymers1,3396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5266
Polymers49,3931
Non-polymers1,1335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.905, 170.367, 121.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Fatty acid decarboxylase


Mass: 49393.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium lipophiloflavum (bacteria)
Gene: HMPREF0298_0515
Details (production host): pGTF2 which encodes GroEL, GroES and Tig chaperones
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0XPZ5

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Non-polymers , 7 types, 1035 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30 % (w/v) PEG4000, 0.2 M MgCl2 and 0.1 M Hepes pH 7.5. The protein was concentrated in Buffer GF containing HEPES, NaCl, 1 mM oleic acid, and 5% Glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.7→49.74 Å / Num. obs: 179979 / % possible obs: 79.3 % / Redundancy: 13.55 % / CC1/2: 0.991 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.153 / Net I/σ(I): 4.02
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.81.016242730.261.3991
1.8-1.930.626229460.4810.8571
1.93-2.080.363209280.750.4951
2.08-2.280.222191430.890.3011
2.28-2.550.162171190.9390.2151
2.55-2.940.129143600.9610.1681
2.94-3.60.08113270.9840.1041
3.6-5.080.05583600.9910.0711
5.08-49.740.05643690.9930.0691

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.95 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 9002 5 %
Rwork0.1683 --
obs0.1697 179979 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9708 0 268 1016 10992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210218
X-RAY DIFFRACTIONf_angle_d1.10213876
X-RAY DIFFRACTIONf_dihedral_angle_d14.4233762
X-RAY DIFFRACTIONf_chiral_restr0.0671488
X-RAY DIFFRACTIONf_plane_restr0.0111840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.48332990.46945667X-RAY DIFFRACTION100
1.72-1.740.43382990.40045688X-RAY DIFFRACTION100
1.74-1.760.38872960.36475613X-RAY DIFFRACTION100
1.76-1.780.36092960.34845640X-RAY DIFFRACTION100
1.78-1.810.34332980.32925644X-RAY DIFFRACTION100
1.81-1.830.32162980.29775677X-RAY DIFFRACTION100
1.83-1.860.29042980.24945653X-RAY DIFFRACTION100
1.86-1.880.2732990.23645673X-RAY DIFFRACTION100
1.88-1.910.27943000.23195699X-RAY DIFFRACTION100
1.91-1.950.27372950.22965613X-RAY DIFFRACTION100
1.95-1.980.24393000.22965704X-RAY DIFFRACTION100
1.98-2.020.26952980.24685649X-RAY DIFFRACTION100
2.02-2.050.25332980.2225695X-RAY DIFFRACTION100
2.05-2.10.21012970.18685642X-RAY DIFFRACTION100
2.1-2.140.23633000.17735689X-RAY DIFFRACTION100
2.14-2.190.21342980.16945673X-RAY DIFFRACTION100
2.19-2.250.20223020.16465729X-RAY DIFFRACTION100
2.25-2.310.18822980.15515672X-RAY DIFFRACTION100
2.31-2.370.19362990.15125675X-RAY DIFFRACTION100
2.37-2.450.17512980.14675670X-RAY DIFFRACTION100
2.45-2.540.19723010.15145718X-RAY DIFFRACTION100
2.54-2.640.19243010.15425715X-RAY DIFFRACTION100
2.64-2.760.19793010.16595708X-RAY DIFFRACTION100
2.76-2.910.19573010.15995733X-RAY DIFFRACTION100
2.91-3.090.19123010.16565708X-RAY DIFFRACTION100
3.09-3.330.2023020.16185748X-RAY DIFFRACTION100
3.33-3.660.16573030.1485750X-RAY DIFFRACTION100
3.66-4.190.14553040.12765781X-RAY DIFFRACTION100
4.19-5.280.1543060.12175815X-RAY DIFFRACTION100
5.28-48.950.15063160.14685985X-RAY DIFFRACTION100

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