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- PDB-9ixl: Crystal structure of the CYP153A double mutant L354T/V456G from M... -

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Basic information

Entry
Database: PDB / ID: 9ixl
TitleCrystal structure of the CYP153A double mutant L354T/V456G from Marinobacter aquaeolei
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Monooxygenase / Metalloprotein
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
LAURIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesMarinobacter nauticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsQin, M.M. / Jiang, Y.P. / Cong, Z.Q. / Zhao, P.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the CYP153A double mutant L354T/V456G from Marinobacter aquaeolei at 2.10 Angstroms resolution
Authors: Qin, M.M. / Jiang, Y.P. / Cong, Z.Q. / Zhao, P.X.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,54411
Polymers110,4502
Non-polymers2,0949
Water6,413356
1
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2265
Polymers55,2251
Non-polymers1,0014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3186
Polymers55,2251
Non-polymers1,0935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.640, 102.020, 223.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cytochrome P450 / CYP153A


Mass: 55224.906 Da / Num. of mol.: 2 / Mutation: L354T,V456G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter nauticus (bacteria) / Gene: DET51_1164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A368UNN3
#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-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M (NH4)2SO4, 0.1 M HEPES 7.0, 26% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→55.96 Å / Num. obs: 67431 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Χ2: 0.97 / Net I/σ(I): 15.1 / Num. measured all: 438492
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.085 / Num. unique obs: 4932 / CC1/2: 0.584 / Rpim(I) all: 0.452 / Χ2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.18.2-3874)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HGD

8hgd


Resolution: 2.1→55.96 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 2001 2.97 %
Rwork0.1962 --
obs0.1968 67365 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→55.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6647 0 144 356 7147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016974
X-RAY DIFFRACTIONf_angle_d1.0879468
X-RAY DIFFRACTIONf_dihedral_angle_d18.8062597
X-RAY DIFFRACTIONf_chiral_restr0.057984
X-RAY DIFFRACTIONf_plane_restr0.0071252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.32471430.31494616X-RAY DIFFRACTION100
2.15-2.210.29421380.29094613X-RAY DIFFRACTION100
2.21-2.280.25841414613X-RAY DIFFRACTION100
2.28-2.350.3061390.26474637X-RAY DIFFRACTION100
2.35-2.430.25661380.25424630X-RAY DIFFRACTION100
2.43-2.530.29631420.25264643X-RAY DIFFRACTION100
2.53-2.650.27051430.2454658X-RAY DIFFRACTION100
2.65-2.790.26521460.24054620X-RAY DIFFRACTION100
2.79-2.960.23821450.22854667X-RAY DIFFRACTION100
2.96-3.190.24941390.22514660X-RAY DIFFRACTION100
3.19-3.510.21711450.1924669X-RAY DIFFRACTION100
3.51-4.020.22291470.17344700X-RAY DIFFRACTION100
4.02-5.060.17231440.14784743X-RAY DIFFRACTION100
5.06-55.960.16991510.16324895X-RAY DIFFRACTION100

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