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- PDB-7y9m: Crystal structure of P450 BM3-2F from Bacillus megaterium -

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Basic information

Entry
Database: PDB / ID: 7y9m
TitleCrystal structure of P450 BM3-2F from Bacillus megaterium
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / synthesis / monooxygenase
Function / homology
Function and homology information


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 / aromatase activity / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
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 / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsWang, Q. / Zhang, L.L. / Liu, W.D. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: to be published
Title: Crystal structure of P450 BM3-2F from Bacillus megaterium
Authors: Wang, Q. / Zhang, L.L. / Liu, W.D. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
History
DepositionJun 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1836
Polymers104,8112
Non-polymers1,3714
Water8,053447
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0913
Polymers52,4061
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-20 kcal/mol
Surface area19440 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0913
Polymers52,4061
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-20 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.767, 146.357, 62.891
Angle α, β, γ (deg.)90.000, 97.280, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 52 or resid 54...
21(chain B and (resid 5 through 40 or (resid 41...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU(chain A and (resid 5 through 52 or resid 54...AA5 - 525 - 52
12SERSERASPASP(chain A and (resid 5 through 52 or resid 54...AA54 - 18254 - 182
13GLNGLNLEULEU(chain A and (resid 5 through 52 or resid 54...AA206 - 262206 - 262
14PHEPHELEULEU(chain A and (resid 5 through 52 or resid 54...AA405 - 455405 - 455
15PHEPHELEULEU(chain A and (resid 5 through 52 or resid 54...AA405 - 455405 - 455
16HEMHEMHOHHOH(chain A and (resid 5 through 52 or resid 54...AC - G501 - 601
21METMETPHEPHE(chain B and (resid 5 through 40 or (resid 41...BB5 - 405 - 40
22LYSLYSLYSLYS(chain B and (resid 5 through 40 or (resid 41...BB4141
23METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
24METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
25METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
26METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
27METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
28METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455

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Components

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


Mass: 52405.730 Da / Num. of mol.: 2 / Mutation: A83F,A329F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria)
Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19
Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pRSF-DuetI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#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-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.64 Å3/Da / Density % sol: 53.49 % / Mosaicity: 0.491 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 25-30% PEG 3350, 0.1M MgCl2, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→25 Å / Num. obs: 56401 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Χ2: 0.642 / Net I/σ(I): 6.1 / Num. measured all: 238806
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.16-2.243.90.39455800.8550.2280.4570.47999.4
2.24-2.334.20.3256320.9170.1780.3670.505100
2.33-2.434.30.25156290.9530.1380.2870.52100
2.43-2.564.30.19656080.970.1070.2240.541100
2.56-2.724.30.15756350.9780.0860.180.559100
2.72-2.934.30.11156610.9880.060.1260.606100
2.93-3.224.30.0856290.9940.0440.0920.672100
3.22-3.694.30.05456670.9970.0290.0610.766100
3.69-4.644.30.04156310.9980.0220.0470.838100
4.64-254.20.0457290.9980.0220.0450.90699.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPA

4kpa


Resolution: 2.16→24.84 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 1984 3.52 %
Rwork0.1728 54361 -
obs0.1743 56345 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.82 Å2 / Biso mean: 38.7024 Å2 / Biso min: 18.7 Å2
Refinement stepCycle: final / Resolution: 2.16→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 96 447 7639
Biso mean--27.37 39.38 -
Num. residues----878
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2560X-RAY DIFFRACTION5.989TORSIONAL
12B2560X-RAY DIFFRACTION5.989TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.230.25331840.20975177536195
2.23-2.320.25531960.192354595655100
2.32-2.430.22582120.184654415653100
2.43-2.560.24081900.182954475637100
2.56-2.720.24961940.187254565650100
2.72-2.930.23522080.190854605668100
2.93-3.220.23711990.188254695668100
3.22-3.680.1852000.16354915691100
3.68-4.640.19161910.144154545645100
4.64-24.840.20212100.170755075717100

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