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- PDB-7wdd: Crystal structure of the P450 BM3 heme domain mutant F87K in comp... -

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Basic information

Entry
Database: PDB / ID: 7wdd
TitleCrystal structure of the P450 BM3 heme domain mutant F87K in complex with N-imidazolyl-hexanoyl-L-phenylalanine, styrene 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 / unspecific monooxygenase / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme 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 / 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 / HYDROXYAMINE / Chem-IC6 / ethenylbenzene / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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. / Cong, Z.
History
DepositionDec 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,75113
Polymers106,8222
Non-polymers2,92911
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-41 kcal/mol
Surface area35160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.820, 148.836, 65.336
Angle α, β, γ (deg.)90.000, 100.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 through 4 and (name N...
21(chain B and (resid 3 through 12 or (resid 13...

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
11LYSLYSGLUGLU(chain A and ((resid 3 through 4 and (name N...AA3 - 45 - 6
12ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
13ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
14ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
15ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
21LYSLYSGLYGLY(chain B and (resid 3 through 12 or (resid 13...BB3 - 125 - 14
22GLUGLUGLUGLU(chain B and (resid 3 through 12 or (resid 13...BB1315
23LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457
24LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457
25LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457
26LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 53410.859 Da / Num. of mol.: 2 / Mutation: F87K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 5 types, 259 molecules

#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: Chemical ChemComp-SYN / ethenylbenzene / styrene


Mass: 104.149 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 53.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, 0.38 M MgCl2, 12-18% PEG3350 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.21→74.42 Å / Num. obs: 53101 / % possible obs: 96.6 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Net I/σ(I): 6.2 / Num. measured all: 178933 / Scaling rejects: 1
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
2.21-2.333.50.4652495271360.840.2870.5482.488.8
7-74.423.40.041571616800.9950.0260.04910.893.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGN

7egn


Resolution: 2.21→39.72 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 3676 3.79 %
Rwork0.1971 93342 -
obs0.1982 53058 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.35 Å2 / Biso mean: 50.8113 Å2 / Biso min: 26.3 Å2
Refinement stepCycle: final / Resolution: 2.21→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 210 248 7348
Biso mean--45.57 49.98 -
Num. residues----880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2674X-RAY DIFFRACTION5.432TORSIONAL
12B2674X-RAY DIFFRACTION5.432TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.240.34081390.29893567370689
2.24-2.270.3772920.31592304239657
2.27-2.310.31261490.27883769391895
2.31-2.340.26621530.27953896404995
2.34-2.380.31981470.26183759390695
2.38-2.420.2791490.24783818396794
2.42-2.460.32261490.25433830397995
2.46-2.50.26921500.24083785393594
2.5-2.550.23161450.24263721386694
2.55-2.60.2341500.24083813396394
2.6-2.660.3051500.23683800395094
2.66-2.720.2691450.24963753389894
2.72-2.790.29061450.2273708385393
2.79-2.860.25311410.22883710385192
2.86-2.950.23721430.23643702384591
2.95-3.040.27621430.2333539368289
3.04-3.150.24441370.22883531366888
3.15-3.280.30531380.22253618375688
3.28-3.430.24031410.21423488362987
3.43-3.610.21231350.18523475361086
3.61-3.830.19931420.1783416355885
3.83-4.130.17811380.16333469360786
4.13-4.550.1761360.13933459359586
4.55-5.20.18281340.14693401353585
5.2-6.550.20041430.18473485362886
6.55-39.720.18461420.15843526366888
Refinement TLS params.Method: refined / Origin x: -5.2343 Å / Origin y: -12.1337 Å / Origin z: 0.3703 Å
111213212223313233
T0.321 Å20.0013 Å20.0013 Å2-0.316 Å20.0116 Å2--0.3153 Å2
L0.1979 °20.1651 °20.0911 °2-0.4035 °20.3366 °2--0.2869 °2
S0.0002 Å °0.0271 Å °0.0064 Å °-0.0272 Å °0.0203 Å °-0.0158 Å °-0.0351 Å °0.0156 Å °-0.018 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 455
2X-RAY DIFFRACTION1allA501 - 801
3X-RAY DIFFRACTION1allB3 - 455
4X-RAY DIFFRACTION1allB501 - 1101
5X-RAY DIFFRACTION1allS1 - 254

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