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- PDB-9uxz: Crystal structure of the P450BM3 triple mutant F87A/L215W/H408W f... -

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Basic information

Entry
Database: PDB / ID: 9uxz
TitleCrystal structure of the P450BM3 triple mutant F87A/L215W/H408W from Priestia megaterium
Components
  • Bifunctional cytochrome P450/NADPH--P450 reductase
  • I7X-PHE-PHE
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Monooxygenase / Metalloprotein
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / METHANOL / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsQin, M.M. / Cong, Z.Q. / Wang, Z.H. / Jiang, Y.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the P450BM3 triple mutant F87A/L215W/H408W from Priestia megaterium at 1.70 Angstroms resolution
Authors: Qin, M.M. / Cong, Z.Q. / Wang, Z.H. / Jiang, Y.P.
History
DepositionMay 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
D: I7X-PHE-PHE
E: I7X-PHE-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,43514
Polymers107,9014
Non-polymers1,53410
Water22,0861226
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
D: I7X-PHE-PHE
hetero molecules

B: Bifunctional cytochrome P450/NADPH--P450 reductase
E: I7X-PHE-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,43514
Polymers107,9014
Non-polymers1,53410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area7190 Å2
ΔGint-84 kcal/mol
Surface area35390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.703, 128.222, 150.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDE

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 53473.875 Da / Num. of mol.: 2 / Mutation: F87A,L215W,H408W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19) (bacteria)
Gene: cyp102A1, cyp102, BG04_163 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Protein/peptide I7X-PHE-PHE


Mass: 476.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 1236 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH4O
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris ph 8.5, 0.38 M MgCl2, 12-18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→150.05 Å / Num. obs: 124547 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.052 / Rrim(I) all: 0.131 / Χ2: 0.76 / Net I/σ(I): 7.4 / Num. measured all: 801072
Reflection shellResolution: 1.7→1.74 Å / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 1.26 / Num. measured all: 51078 / Num. unique obs: 9072 / CC1/2: 0.601 / Rpim(I) all: 0.575 / Rrim(I) all: 1.39 / Χ2: 0.74 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→54.67 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1998 1.61 %
Rwork0.1851 --
obs0.1855 124196 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→54.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 0 104 1226 8612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047661
X-RAY DIFFRACTIONf_angle_d0.75310416
X-RAY DIFFRACTIONf_dihedral_angle_d17.5782825
X-RAY DIFFRACTIONf_chiral_restr0.0461115
X-RAY DIFFRACTIONf_plane_restr0.0051352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.28541400.27158591X-RAY DIFFRACTION99
1.74-1.790.27641410.25288593X-RAY DIFFRACTION99
1.79-1.840.28051420.2388620X-RAY DIFFRACTION99
1.84-1.90.24411410.23018629X-RAY DIFFRACTION99
1.9-1.970.24931410.21798597X-RAY DIFFRACTION99
1.97-2.050.22431420.19918684X-RAY DIFFRACTION99
2.05-2.140.21461420.19158690X-RAY DIFFRACTION99
2.14-2.250.23351430.1848708X-RAY DIFFRACTION100
2.25-2.40.21621410.18868662X-RAY DIFFRACTION99
2.4-2.580.2321430.18578773X-RAY DIFFRACTION100
2.58-2.840.18951430.18078760X-RAY DIFFRACTION99
2.84-3.250.22781430.17778815X-RAY DIFFRACTION99
3.25-4.10.14881460.15528896X-RAY DIFFRACTION100
4.1-54.670.19411500.16729180X-RAY DIFFRACTION99

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