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

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Basic information

Entry
Database: PDB / ID: 7wdh
TitleCrystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanine, phenol 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 / 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 / PHENOL / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Engineering Cytochrome P450BM3 Enzymes for Direct Nitration of Unsaturated Hydrocarbons.
Authors: Wang, X. / Lin, X. / Jiang, Y. / Qin, X. / Ma, N. / Yao, F. / Dong, S. / Liu, C. / Feng, Y. / Jin, L. / Xian, M. / Cong, Z.
History
DepositionDec 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Nov 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

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)109,98117
Polymers106,7062
Non-polymers3,27515
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-42 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.893, 148.005, 65.467
Angle α, β, γ (deg.)90.000, 100.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 30 or (resid 31...
21(chain B and (resid 3 through 108 or (resid 109...

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
11LYSLYSMETMET(chain A and (resid 3 through 30 or (resid 31...AA3 - 305 - 32
12LYSLYSLYSLYS(chain A and (resid 3 through 30 or (resid 31...AA3133
13LYSLYSLEULEU(chain A and (resid 3 through 30 or (resid 31...AA3 - 4555 - 457
14LYSLYSLEULEU(chain A and (resid 3 through 30 or (resid 31...AA3 - 4555 - 457
15LYSLYSLEULEU(chain A and (resid 3 through 30 or (resid 31...AA3 - 4555 - 457
16LYSLYSLEULEU(chain A and (resid 3 through 30 or (resid 31...AA3 - 4555 - 457
21LYSLYSSERSER(chain B and (resid 3 through 108 or (resid 109...BB3 - 1085 - 110
22GLNGLNALAALA(chain B and (resid 3 through 108 or (resid 109...BB109 - 111111 - 113
23ILEILELEULEU(chain B and (resid 3 through 108 or (resid 109...BB2 - 4554 - 457
24ILEILELEULEU(chain B and (resid 3 through 108 or (resid 109...BB2 - 4554 - 457
25ILEILELEULEU(chain B and (resid 3 through 108 or (resid 109...BB2 - 4554 - 457
26ILEILELEULEU(chain B and (resid 3 through 108 or (resid 109...BB2 - 4554 - 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: 53352.758 Da / Num. of mol.: 2 / Mutation: F87A
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, 766 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-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 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: 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: 1.68→74 Å / Num. obs: 121516 / % possible obs: 96.6 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Net I/σ(I): 11.6 / Num. measured all: 415780 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.770.49864090177130.8120.3050.5842.596.7
5.3-740.0351414039080.9980.0220.04226.196.3

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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: 1.68→37.57 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 3478 1.64 %
Rwork0.1787 208259 -
obs0.179 120459 84.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.71 Å2 / Biso mean: 32.8952 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: final / Resolution: 1.68→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 235 751 7926
Biso mean--26.78 41.67 -
Num. residues----892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4235X-RAY DIFFRACTION4.634TORSIONAL
12B4235X-RAY DIFFRACTION4.634TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.70.30281480.28198345849385
1.7-1.720.27671360.27598437857385
1.72-1.750.23881390.2598352849186
1.75-1.780.30391370.25948509864686
1.78-1.80.2941390.25318333847285
1.8-1.840.30771440.24098388853285
1.84-1.870.23751400.23188440858086
1.87-1.910.24941350.22578459859485
1.91-1.940.23071400.21358478861887
1.94-1.990.26531350.21098397853285
1.99-2.030.23251320.20138491862385
2.03-2.080.25851390.19658265840485
2.08-2.140.22661390.19338304844384
2.14-2.20.21221420.18738218836083
2.2-2.270.20211380.18528187832583
2.27-2.350.19461440.18638112825683
2.36-2.450.19571350.1848070820582
2.45-2.560.2061350.17938045818082
2.56-2.70.20521370.19058026816382
2.7-2.860.2061370.18018131826883
2.86-3.090.20631360.18448150828682
3.09-3.40.17481410.16948273841484
3.4-3.890.16441380.15138301843984
3.89-4.90.18671410.14298638877988
4.9-37.570.17011510.16668910906190

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