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- PDB-8b2p: CYP153A71 from Acinetobacter dieselolei bound to octanoic acid -

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Basic information

Entry
Database: PDB / ID: 8b2p
TitleCYP153A71 from Acinetobacter dieselolei bound to octanoic acid
ComponentsCytochrome P450 alkane hydroxylase
KeywordsOXIDOREDUCTASE / Alkane hydroxylase Cytochrome P450 monooxygenase CYP153 Octanoic acid
Function / homology
Function and homology information


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, 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 / OCTANOIC ACID (CAPRYLIC ACID) / Cytochrome P450 alkane hydroxylase
Similarity search - Component
Biological speciesAlcanivorax dieselolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsOpperman, D.J. / Tolmie, C.
Funding support United Kingdom, South Africa, 3items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
National Research Foundation in South Africa112094 South Africa
Department of Science and Innovation, South Africac*change, PAR-02 South Africa
CitationJournal: Catalysts / Year: 2022
Title: CYP153A71 from Alcanivorax dieselolei: Oxidation beyond Monoterminal Hydroxylation of n-Alkanes
Authors: Jacobs, C.L. / do Aido-Machado, R. / Tolmie, C. / Smit, M.S. / Opperman, D.J.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 alkane hydroxylase
B: Cytochrome P450 alkane hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2856
Polymers107,7632
Non-polymers1,5214
Water5,062281
1
A: Cytochrome P450 alkane hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6423
Polymers53,8821
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 alkane hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6423
Polymers53,8821
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.661, 76.817, 107.344
Angle α, β, γ (deg.)90.000, 90.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 49 - 468 / Label seq-ID: 49 - 468

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cytochrome P450 alkane hydroxylase


Mass: 53881.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcanivorax dieselolei (bacteria) / Gene: p450 / Production host: Escherichia coli (E. coli) / References: UniProt: D0Q1H3
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5 12% (w/v) polyethylene glycol 3350 10 mM octanoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→46.11 Å / Num. obs: 66934 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.083 / Rrim(I) all: 0.154 / Net I/σ(I): 7.2 / Num. measured all: 227101 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-23.51.3651556644660.5190.8571.6151.297
9.15-46.113.20.03622256910.9970.0240.04324.797.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.08 Å46.11 Å
Translation5.08 Å46.11 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FYF

5fyf


Resolution: 1.95→46.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2547 / WRfactor Rwork: 0.2119 / FOM work R set: 0.5859 / SU B: 11.558 / SU ML: 0.277 / SU R Cruickshank DPI: 0.2104 / SU Rfree: 0.1831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 3379 5 %RANDOM
Rwork0.229 ---
obs0.2311 63554 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.25 Å2 / Biso mean: 40.926 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å23.75 Å2
2---2.65 Å20 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 1.95→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 106 285 7234
Biso mean--27.5 41.17 -
Num. residues----844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137167
X-RAY DIFFRACTIONr_bond_other_d0.0050.0156815
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.6689709
X-RAY DIFFRACTIONr_angle_other_deg1.121.59615659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01921.494435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.847151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.641570
X-RAY DIFFRACTIONr_chiral_restr0.0510.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028154
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021762
Refine LS restraints NCS

Ens-ID: 1 / Number: 14481 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 264 -
Rwork0.386 4632 -
all-4896 -
obs--97.05 %

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