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- PDB-9l7u: Crystal structure of P450 BM3 F87A/V78S/L75N mutant complex with ... -

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Basic information

Entry
Database: PDB / ID: 9l7u
TitleCrystal structure of P450 BM3 F87A/V78S/L75N mutant complex with (-)-Ambroxide
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome p450
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / 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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDong, S. / Feng, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071266 China
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: Innov Life / Year: 2026
Title: Structural insights into the functional convergence of two divergent cytochrome P450 enzymes
Authors: Ma, L. / Dong, S. / Zhang, J. / Liu, M. / Li, Y. / Feng, X. / Zhang, H. / Peng, W. / Feng, Y. / Li, S.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 2.0Apr 8, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / struct_conf / struct_conn / struct_sheet_range
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value ..._entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.value / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jul 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Aug 12, 2026Group: Database references / Derived calculations
Category: citation / pdbx_nonpoly_atom_coordination ...citation / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _citation.country / _citation.journal_id_ISSN / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)106,1336
Polymers104,4272
Non-polymers1,7064
Water5,152286
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0663
Polymers52,2131
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-20 kcal/mol
Surface area19560 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0663
Polymers52,2131
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-21 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.175, 158.219, 58.723
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52213.453 Da / Num. of mol.: 2 / Mutation: L76N,V79S,F88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2Q7T0, 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
#3: Chemical ChemComp-A1EI5 / (3~{a}~{R},5~{a}~{S},9~{a}~{S},9~{b}~{R})-3~{a},6,6,9~{a}-tetramethyl-2,4,5,5~{a},7,8,9,9~{b}-octahydro-1~{H}-benzo[e][1]benzofuran / (-)-ambroxide


Mass: 236.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH7.5, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.7→79.11 Å / Num. obs: 28387 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.956 / Rmerge(I) obs: 0.329 / Rpim(I) all: 0.146 / Rrim(I) all: 0.361 / Χ2: 1 / Net I/σ(I): 6.2 / Num. measured all: 167251
Reflection shellResolution: 2.7→2.85 Å / % possible obs: 98.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.786 / Num. measured all: 19371 / Num. unique obs: 4124 / CC1/2: 0.625 / Rpim(I) all: 0.399 / Rrim(I) all: 0.884 / Χ2: 0.87 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→79.11 Å / Cross valid method: FREE R-VALUE / σ(F): 194.94 / Phase error: 30.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.275 2107 7.46 %
Rwork0.2309 --
obs0.2354 28249 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→79.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 120 294 7652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037542
X-RAY DIFFRACTIONf_angle_d0.76510244
X-RAY DIFFRACTIONf_dihedral_angle_d7.5751019
X-RAY DIFFRACTIONf_chiral_restr0.0451103
X-RAY DIFFRACTIONf_plane_restr0.0051323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.30791360.271730X-RAY DIFFRACTION91
2.76-2.830.29981400.24591763X-RAY DIFFRACTION92
2.83-2.910.27641320.2661752X-RAY DIFFRACTION92
2.91-2.990.32731360.24991757X-RAY DIFFRACTION93
2.99-3.090.32511410.25961756X-RAY DIFFRACTION92
3.09-3.20.33311170.25811761X-RAY DIFFRACTION93
3.2-3.330.31371480.23941754X-RAY DIFFRACTION92
3.33-3.480.28341250.24081753X-RAY DIFFRACTION92
3.48-3.660.32451390.2381731X-RAY DIFFRACTION90
3.66-3.890.26181350.23961729X-RAY DIFFRACTION92
3.89-4.190.26021410.20361763X-RAY DIFFRACTION92
4.19-4.620.24231350.20161749X-RAY DIFFRACTION92
4.62-5.280.24991450.20531771X-RAY DIFFRACTION91
5.28-6.660.26871380.25281705X-RAY DIFFRACTION90
6.66-79.110.20491360.20281731X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16170.13040.08370.6122-0.11950.8089-0.0039-0.0437-0.0776-0.1330.07230.1919-0.0003-0.1998-0.01010.26330.04650.04190.32390.01920.044811.596817.59345.8743
21.0016-0.2169-0.12970.78750.59611.17320.0730.1579-0.1522-0.136-0.16360.3471-0.218-0.5320.07480.56570.11250.00250.3138-0.01020.1187.889939.09675.6946
30.4155-0.11730.3590.5318-0.01581.28340.0430.0508-0.1062-0.0340.0456-0.0952-0.1313-0.1378-0.03750.2457-0.00270.07020.18-0.01090.054921.721323.393411.75
41.3950.75930.41111.01140.43141.10830.00810.0130.07860.0443-0.01270.0742-0.3502-0.15680.05220.37460.04970.060.2675-0.00120.087213.244933.441425.2999
50.53140.0526-0.16760.6702-0.10941.3248-0.0554-0.18860.0334-0.21650.1224-0.171-0.39080.3775-0.00290.3164-0.0284-0.02720.237-0.00750.079850.792411.492935.0549
60.66330.2814-0.64141.4105-2.26613.7321-0.0994-0.07780.04410.03120.19260.22770.0268-0.4383-0.04650.3664-0.0568-0.02520.185-0.00340.089230.7789-11.016430.7366
70.8310.1267-0.44490.58590.37180.8777-0.009-0.1442-0.0420.16030.01750.03360.33380.2302-0.00260.51990.0829-0.02830.2138-0.05420.070438.4582-18.331144.3321
81.77610.823-0.92571.6846-0.63240.964-0.1663-0.2783-0.12560.3639-0.0293-0.30220.30620.2690.05490.36330.06410.02110.1401-0.00340.141848.0225-17.153434.9961
90.9423-0.4260.08941.2926-0.131.7244-0.06650.04660.0347-0.1712-0.0162-0.26320.2570.16390.07740.1984-0.01670.09410.3025-0.01180.204545.8164-13.519120.9637
100.2890.3368-0.40850.52-0.59460.681-0.10720.050.05270.0324-0.09580.0571-0.09330.1934-0.07610.1768-0.04470.07280.25540.01160.082939.8765-7.548537.8346
110.78040.5978-0.43710.7458-0.93181.78370.009-0.07250.05990.13340.00250.0909-0.0052-0.28710.02570.22020.0350.0360.2357-0.03590.112327.4641-3.361745.2876
120.72780.4521-0.47390.5848-0.77092.21430.0811-0.10670.19170.2681-0.12550.1918-0.43440.0330.03620.4005-0.01820.05650.2468-0.03540.125438.570914.484440.7206
130.56210.2337-0.20460.43-0.59311.4848-0.0351-0.0198-0.02820.2574-0.00540.1521-0.2818-0.04770.00750.2161-0.00560.07330.2495-0.04970.076830.9901-3.277340.2852
142.08060.8553-0.09092.0495-0.81271.0947-0.21570.1088-0.32970.02230.0223-0.20990.1441-0.30480.19560.2644-0.0760.06940.2311-0.0060.113939.5926-10.876152.7469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 131 )
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 226 )
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 424 )
4X-RAY DIFFRACTION4chain 'A' and (resid 425 through 455 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 131 )
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 158 )
8X-RAY DIFFRACTION8chain 'B' and (resid 159 through 188 )
9X-RAY DIFFRACTION9chain 'B' and (resid 189 through 252 )
10X-RAY DIFFRACTION10chain 'B' and (resid 253 through 282 )
11X-RAY DIFFRACTION11chain 'B' and (resid 283 through 335 )
12X-RAY DIFFRACTION12chain 'B' and (resid 336 through 384 )
13X-RAY DIFFRACTION13chain 'B' and (resid 385 through 424 )
14X-RAY DIFFRACTION14chain 'B' and (resid 425 through 455 )

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