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- PDB-8hkd: Crystal structure of P450BSbeta-L78G/Q85F/F173S/G290I variant in ... -

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Basic information

Entry
Database: PDB / ID: 8hkd
TitleCrystal structure of P450BSbeta-L78G/Q85F/F173S/G290I variant in complex with palmitoleic acid
ComponentsFatty-acid peroxygenase
KeywordsHYDROLASE / P450 hydroxylase
Function / homology
Function and homology information


fatty-acid peroxygenase / 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 / PALMITOLEIC ACID / DI(HYDROXYETHYL)ETHER / Fatty-acid peroxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHe, C. / Wang, X. / Li, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Synth / Year: 2023
Title: Biocatalytic enantioselective gamma-C-H lactonization of aliphatic carboxylic acids
Authors: Ma, Q. / Shan, X. / Chu, X. / Xu, H. / Chen, Z. / Li, F. / Liao, J. / He, C. / Bai, W. / Wang, X.
History
DepositionNov 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty-acid peroxygenase
B: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,80312
Polymers98,4242
Non-polymers2,37910
Water6,215345
1
A: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2955
Polymers49,2121
Non-polymers1,0834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-21 kcal/mol
Surface area17950 Å2
MethodPISA
2
B: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5087
Polymers49,2121
Non-polymers1,2956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-21 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.843, 126.843, 146.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-506-

PEG

21B-787-

HOH

31B-856-

HOH

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Components

#1: Protein Fatty-acid peroxygenase / Cytochrome P450 152A1 / Cytochrome P450BsBeta / Fatty acid beta-hydroxylase


Mass: 49212.145 Da / Num. of mol.: 2 / Mutation: L78G, Q85F, F173S, G290I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: cypC, CYP152A1, BSU02100 / Production host: Escherichia coli (E. coli) / References: UniProt: O31440, fatty-acid peroxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES pH 7.3, 28 % PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.35→13.21 Å / Num. obs: 56832 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Χ2: 0.95 / Net I/σ(I): 13.1 / Num. measured all: 391198
Reflection shellResolution: 2.35→2.42 Å / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 1.201 / Num. measured all: 22593 / Num. unique obs: 4631 / CC1/2: 0.516 / Rpim(I) all: 0.603 / Rrim(I) all: 1.348 / Χ2: 0.96 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→13.21 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 2919 5.14 %
Rwork0.1911 --
obs0.193 56806 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→13.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 164 345 7103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086927
X-RAY DIFFRACTIONf_angle_d0.8929344
X-RAY DIFFRACTIONf_dihedral_angle_d15.3342595
X-RAY DIFFRACTIONf_chiral_restr0.048955
X-RAY DIFFRACTIONf_plane_restr0.0081201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.390.33371230.28892544X-RAY DIFFRACTION100
2.39-2.430.33681670.27912495X-RAY DIFFRACTION100
2.43-2.470.31091370.27542545X-RAY DIFFRACTION100
2.47-2.520.28781450.25542525X-RAY DIFFRACTION100
2.52-2.570.30531560.25622533X-RAY DIFFRACTION100
2.57-2.630.27691390.2462547X-RAY DIFFRACTION100
2.63-2.690.28641120.24332576X-RAY DIFFRACTION100
2.69-2.750.30351390.23532552X-RAY DIFFRACTION100
2.75-2.830.25141190.22182551X-RAY DIFFRACTION100
2.83-2.910.24261370.22312565X-RAY DIFFRACTION100
2.91-30.22261530.2222540X-RAY DIFFRACTION100
3-3.110.24621120.21512588X-RAY DIFFRACTION100
3.11-3.230.2511280.20512562X-RAY DIFFRACTION100
3.23-3.380.25651330.19752553X-RAY DIFFRACTION100
3.38-3.550.24221300.18812595X-RAY DIFFRACTION100
3.55-3.770.20521340.16872570X-RAY DIFFRACTION100
3.77-4.050.18391530.15892571X-RAY DIFFRACTION100
4.05-4.450.17821530.1462563X-RAY DIFFRACTION100
4.45-5.060.20511490.14492592X-RAY DIFFRACTION100
5.06-6.250.20951450.17072637X-RAY DIFFRACTION100
6.26-13.210.17291550.1532683X-RAY DIFFRACTION99
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)
11.1033-0.42230.25941.3931-0.63321.5640.0715-0.5475-0.34070.0679-0.01430.16250.4156-0.2171-0.04810.7274-0.10870.10110.70740.16330.3454-17.809448.811151.7796
22.0256-0.3836-0.38521.6240.34621.1379-0.0885-0.074-0.35730.2207-0.070.34410.1594-0.14310.08850.1937-0.01740.05990.1916-0.01390.38678.476444.42711.4078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 13 through 416)
2X-RAY DIFFRACTION2(chain 'B' and resid 11 through 416)

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