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- PDB-7yjd: Crystal structure of the P450 BM3 heme domain mutant F87A in comp... -

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Basic information

Entry
Database: PDB / ID: 7yjd
TitleCrystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanine and hydroxylamine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain / Complex
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 / HYDROXYAMINE / Chem-IC6 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778060 China
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: To Be Published
Title: Crystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanine and hydroxylamine
Authors: Jiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
History
DepositionJul 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)109,32210
Polymers106,7062
Non-polymers2,6178
Water19,5101083
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-42 kcal/mol
Surface area34520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.516, 148.063, 64.758
Angle α, β, γ (deg.)90.000, 100.090, 90.000
Int Tables number4
Space group name H-MP1211

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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: 53352.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512
Gene: cyp102A1, cyp102, BG04_163 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: 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
#3: Chemical ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IC6 / (2S)-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid


Mass: 329.394 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.38M MgCl2, 0.1M Tris 8.5, 12-18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 85282 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Χ2: 0.86 / Net I/σ(I): 6.9 / Num. measured all: 571382
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.936.40.86241950.8080.3610.9360.8199
1.93-1.976.20.742360.8540.2960.7610.82798.6
1.97-2.015.80.5641160.8780.2430.6120.80196.6
2.01-2.056.30.51542130.8930.2160.5590.83498
2.05-2.0970.41742970.9250.1680.450.813100
2.09-2.1470.35642530.9420.1440.3840.835100
2.14-2.1970.29942800.960.120.3220.8599.9
2.19-2.2570.24343180.9730.0980.2620.83699.9
2.25-2.326.90.20742910.9760.0840.2240.8499.8
2.32-2.396.90.17942510.9830.0720.1930.86999.9
2.39-2.486.90.1442970.9890.0570.1520.81799.6
2.48-2.586.90.1242840.990.0480.130.85499.7
2.58-2.76.60.09842520.9930.040.1060.79699.3
2.7-2.8460.07642370.9950.0320.0830.83998.1
2.84-3.026.50.06742160.9960.0270.0730.85998.9
3.02-3.257.20.05643270.9970.0220.0610.966100
3.25-3.587.10.04742820.9980.0190.0511.07899.9
3.58-4.0970.0443010.9980.0160.0431.12299.7
4.09-5.166.50.0342850.9990.0120.0320.88299.1
5.16-506.80.02543510.9990.010.0270.6399.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGN

7egn


Resolution: 1.9→28.81 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 1987 2.4 %
Rwork0.1851 80691 -
obs0.1858 82678 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.89 Å2 / Biso mean: 25.004 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 1.9→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 186 1083 8325
Biso mean--13.45 34.98 -
Num. residues----892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.34651210.30664889501082
1.95-20.27411280.2755221534989
2-2.060.30831390.24655630576996
2.06-2.130.24061460.231959516097100
2.13-2.20.26551450.211959106055100
2.2-2.290.22231460.20958966042100
2.29-2.390.26911460.198459366082100
2.39-2.520.24411450.19458966041100
2.52-2.680.24411450.18715896604199
2.68-2.880.21871420.18285788593098
2.88-3.170.19931470.178759396086100
3.17-3.630.19141470.161559616108100
3.63-4.570.15111440.13955914605899
4.57-28.810.16641460.16385864601098

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