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- PDB-5yhj: Cytochrome P450EX alpha (CYP152N1) wild-type with myristic acid -

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Basic information

Entry
Database: PDB / ID: 5yhj
TitleCytochrome P450EX alpha (CYP152N1) wild-type with myristic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Fatty Acid Peroxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MYRISTIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesExiguobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOnoda, H. / Shoji, O. / Suzuki, K. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16J02846 Japan
The Ministry of Education,Culture,Sports,Science and Technology(MEXT)15H05806 Japan
The Ministry of Education,Culture,Sports,Science and Technology(MEXT)17H03087 Japan
CitationJournal: Catalysis Science And Technology / Year: 2017
Title: Alpha-Oxidative Decarboxylation of Fatty Acids Catalysed by Cytochrome P450 Peroxygenases Yielding Shorter-Alkyl-Chain Fatty Acids
Authors: Onoda, H. / Shoji, O. / Suzuki, K. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionSep 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0166
Polymers95,3262
Non-polymers1,6904
Water1,06359
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5083
Polymers47,6631
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5083
Polymers47,6631
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-48 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.962, 58.962, 238.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Cytochrome P450 /


Mass: 47663.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sp. (strain ATCC BAA-1283 / AT1b) (bacteria)
Strain: ATCC BAA-1283 / AT1b / Gene: EAT1b_2299 / Plasmid: pQE30t-CYP152N1
Details (production host): Thrombin_cleavage_site-BamHI-CYP152N1-ter-HindII
Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: C4L2G9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 uL Protein solution (16 mg/ml CYP152N1, 0.05 M MES buffer pH 7.0, 20% v/v Glycerol) and 1 uL (0.1M Tris-HCl buffer pH 8.5, 0.2M Magnesium chloride, 30% w/v polyethylene glycol 4000 (Pre- ...Details: 1 uL Protein solution (16 mg/ml CYP152N1, 0.05 M MES buffer pH 7.0, 20% v/v Glycerol) and 1 uL (0.1M Tris-HCl buffer pH 8.5, 0.2M Magnesium chloride, 30% w/v polyethylene glycol 4000 (Pre-Crystallization Test Reagent A2, Hampton Research)
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 35823 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.95 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 1.094 / Net I/av σ(I): 29.79 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.70.335.0936220.9810.1360.3571.026100
2.38-2.486.80.2466.6235680.990.1020.2671.012100
2.48-2.596.80.1899.4235870.9940.0780.2051.094100
2.59-2.736.80.14611.7535630.9940.060.1581.071100
2.73-2.96.80.10815.4335920.9960.0450.1171.056100
2.9-3.126.80.07520.8236120.9980.0310.0811.04499.9
3.12-3.436.80.05329.2235740.9990.0220.0571.059100
3.43-3.936.80.0393836010.9990.0160.0421.15799.9
3.93-4.936.70.03145.7835960.9990.0130.0341.22899.4
4.93-206.60.03344.7135080.9990.0140.0361.19296.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.746 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.85
RfactorNum. reflection% reflection
Rfree0.2478 1986 5.56 %
Rwork0.2142 --
obs0.2161 35736 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.6 Å2 / Biso mean: 57.8494 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 2.3→19.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 118 59 6834
Biso mean--49.89 42.99 -
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096948
X-RAY DIFFRACTIONf_angle_d1.0489415
X-RAY DIFFRACTIONf_chiral_restr0.052995
X-RAY DIFFRACTIONf_plane_restr0.0061211
X-RAY DIFFRACTIONf_dihedral_angle_d17.5214122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2991-2.35650.3441410.27982425256699
2.3565-2.42010.31061390.265623682507100
2.4201-2.49120.29661400.248424282568100
2.4912-2.57150.35031510.239124172568100
2.5715-2.66320.27661420.240924172559100
2.6632-2.76950.28041430.240724012544100
2.7695-2.89520.3081410.237924242565100
2.8952-3.04730.23211420.234824042546100
3.0473-3.23750.29761380.230524462584100
3.2375-3.48620.24091460.228524272573100
3.4862-3.83470.26071400.202124072547100
3.8347-4.38430.19181390.182324352574100
4.3843-5.50380.21191420.1792410255299
5.5038-19.74650.22361420.20822341248396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75570.6407-1.54790.80670.62733.8825-0.38730.5086-0.3384-0.04250.00830.08751.7018-0.61870.27840.7841-0.30390.06340.3981-0.06470.39284.84341.0395-17.7568
22.26482.0151-0.05942.5764-1.10156.0719-0.5039-0.6116-0.4629-0.29630.0911-0.11512.2515-0.44760.27881.1201-0.25060.23050.08560.06410.4665-0.7703-7.686610.0766
33.28021.0383-1.47220.611-0.20726.3164-0.34150.67410.2802-0.06130.35610.33970.3951-0.86230.06770.3044-0.1258-0.03120.32660.04220.3705-1.56939.5976-3.0726
43.91950.4386-1.77552.15830.5726.4323-0.1117-0.78540.14560.2313-0.13010.03450.49220.73670.23690.2413-0.0222-0.02630.3176-0.0170.336812.668613.962610.8509
51.42010.66490.65861.7215-1.51082.9189-0.05420.12050.03060.4126-0.3287-0.3455-0.60031.57920.28350.4216-0.2916-0.07420.8120.06560.426528.402624.5795-7.2575
62.72471.493-1.39643.1981-0.24885.99020.1338-0.5077-0.1943-0.2489-0.4343-0.6589-0.19172.15470.14540.1268-0.1390.03141.0340.1750.457135.574229.1856-33.9495
70.48830.9101-0.36083.2512-1.90296.09320.4082-0.12980.34840.769-0.37870.2941-1.0790.05950.03280.4312-0.12510.07420.2685-0.07160.392917.721932.1551-19.8939
82.6740.28581.09164.3142-2.01917.4402-0.05830.24610.1057-0.81440.00430.08150.67850.42180.16060.3214-0.01220.00430.3007-0.00530.315715.481416.7977-35.8816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )A2 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 226 )A89 - 226
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 377 )A227 - 377
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 412 )A378 - 412
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 88 )B2 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 257 )B89 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 377 )B258 - 377
8X-RAY DIFFRACTION8chain 'B' and (resid 378 through 412 )B378 - 412

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