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- PDB-7wdg: Crystal structure of the P450 BM3 heme domain mutant F87L in comp... -

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Basic information

Entry
Database: PDB / ID: 7wdg
TitleCrystal structure of the P450 BM3 heme domain mutant F87L 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


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / 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 / PHENOL / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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)109,97116
Polymers106,7902
Non-polymers3,18114
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-43 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.951, 148.035, 65.297
Angle α, β, γ (deg.)90.000, 99.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 34 or (resid 35...
21(chain B and ((resid 2 through 4 and (name N...

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
11ILEILEASPASP(chain A and (resid 2 through 34 or (resid 35...AA2 - 344 - 36
12GLUGLUGLUGLU(chain A and (resid 2 through 34 or (resid 35...AA3537
13ILEILELEULEU(chain A and (resid 2 through 34 or (resid 35...AA2 - 4554 - 457
14ILEILELEULEU(chain A and (resid 2 through 34 or (resid 35...AA2 - 4554 - 457
15ILEILELEULEU(chain A and (resid 2 through 34 or (resid 35...AA2 - 4554 - 457
21ILEILEGLUGLU(chain B and ((resid 2 through 4 and (name N...BB2 - 44 - 6
22ILEILELEULEU(chain B and ((resid 2 through 4 and (name N...BB2 - 4554 - 457
23ILEILELEULEU(chain B and ((resid 2 through 4 and (name N...BB2 - 4554 - 457
24ILEILELEULEU(chain B and ((resid 2 through 4 and (name N...BB2 - 4554 - 457
25ILEILELEULEU(chain B and ((resid 2 through 4 and (name N...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: 53394.836 Da / Num. of mol.: 2 / Mutation: F87L
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, 359 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-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 53.2 %
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: 2.07→74.02 Å / Num. obs: 65679 / % possible obs: 97.5 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.052 / Rrim(I) all: 0.097 / Net I/σ(I): 9.4 / Num. measured all: 223952 / Scaling rejects: 27
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
2.07-2.183.60.5883538398000.740.3590.6892.599.4
6.53-74.023.50.038750121320.9960.0240.04521.497.9

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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: 2.07→58.07 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 3376 3.05 %
Rwork0.2009 115679 -
obs0.2017 65213 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.39 Å2 / Biso mean: 46.0302 Å2 / Biso min: 22.34 Å2
Refinement stepCycle: final / Resolution: 2.07→58.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 228 345 7573
Biso mean--38.89 46.27 -
Num. residues----896
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2728X-RAY DIFFRACTION3.195TORSIONAL
12B2728X-RAY DIFFRACTION3.195TORSIONAL
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 (%)
2.07-2.090.33751430.32124661480493
2.09-2.120.37361430.31234645478892
2.12-2.150.32091460.31024571471793
2.15-2.180.28111440.28464627477192
2.18-2.220.30171480.28274571471993
2.22-2.250.33481470.27644635478293
2.25-2.290.3261410.27414538467993
2.29-2.340.31181550.26724640479592
2.34-2.380.24081410.25464584472592
2.38-2.430.27571480.24924587473592
2.43-2.480.28351380.2414496463491
2.48-2.540.28451430.23144555469892
2.54-2.60.29441400.2294511465191
2.6-2.670.25871440.23674488463290
2.67-2.750.25661380.22154416455489
2.75-2.840.22951350.21794362449787
2.84-2.940.24421440.22644311445587
2.94-3.060.26711270.22294158428584
3.06-3.20.25361330.2154150428384
3.2-3.370.23561310.214227435885
3.37-3.580.23071320.17254139427183
3.58-3.860.19041330.16774177431084
3.86-4.240.16931330.15814335446887
4.24-4.860.14661340.14394272440686
4.86-6.120.20971360.18044411454789
6.12-58.070.18041430.16574612475593
Refinement TLS params.Method: refined / Origin x: -5.366 Å / Origin y: -11.7891 Å / Origin z: 0.5099 Å
111213212223313233
T0.2843 Å2-0.0083 Å20.0102 Å2-0.2759 Å20.0126 Å2--0.2638 Å2
L0.3536 °20.1581 °20.1448 °2-0.391 °20.2237 °2--0.1647 °2
S-0.0118 Å °0.0353 Å °0.0133 Å °0.0018 Å °0.0233 Å °0.0056 Å °-0.0034 Å °0.0137 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 455
2X-RAY DIFFRACTION1allA501 - 1101
3X-RAY DIFFRACTION1allB2 - 455
4X-RAY DIFFRACTION1allB501 - 1101
5X-RAY DIFFRACTION1allS1 - 345

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