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- PDB-7y0t: Crystal structure of the P450 BM3 heme domain mutant F87A in comp... -

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Basic information

Entry
Database: PDB / ID: 7y0t
TitleCrystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanyl-L-phenylalanine
Components
  • Bifunctional cytochrome P450/NADPH--P450 reductase
  • I7X-PHE-PHE
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 / 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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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: Anchoring a Structurally Editable Proximal Cofactor-like Module to Construct an Artificial Dual-center Peroxygenase.
Authors: Qin, X. / Jiang, Y. / Yao, F. / Chen, J. / Kong, F. / Zhao, P. / Jin, L. / Cong, Z.
History
DepositionJun 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Bifunctional cytochrome P450/NADPH--P450 reductase
A: Bifunctional cytochrome P450/NADPH--P450 reductase
C: I7X-PHE-PHE
D: I7X-PHE-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8926
Polymers107,6594
Non-polymers1,2332
Water11,584643
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.483, 144.354, 63.236
Angle α, β, γ (deg.)90.000, 100.340, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 88 or resid 90...
21(chain B and (resid 3 through 88 or resid 90...

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
11LYSLYSTHRTHR(chain A and (resid 3 through 88 or resid 90...AB3 - 885 - 90
12TRPTRPPROPRO(chain A and (resid 3 through 88 or resid 90...AB90 - 10592 - 107
13PHEPHEALAALA(chain A and (resid 3 through 88 or resid 90...AB107 - 117109 - 119
14METMETMETMET(chain A and (resid 3 through 88 or resid 90...AB119121
15LYSLYSLEULEU(chain A and (resid 3 through 88 or resid 90...AB3 - 4555 - 457
16LYSLYSLEULEU(chain A and (resid 3 through 88 or resid 90...AB3 - 4555 - 457
17LYSLYSLEULEU(chain A and (resid 3 through 88 or resid 90...AB3 - 4555 - 457
18LYSLYSLEULEU(chain A and (resid 3 through 88 or resid 90...AB3 - 4555 - 457
19LYSLYSLEULEU(chain A and (resid 3 through 88 or resid 90...AB3 - 4555 - 457
21LYSLYSTHRTHR(chain B and (resid 3 through 88 or resid 90...BA3 - 885 - 90
22TRPTRPPROPRO(chain B and (resid 3 through 88 or resid 90...BA90 - 10592 - 107
23PHEPHEGLNGLN(chain B and (resid 3 through 88 or resid 90...BA107 - 109109 - 111
24GLNGLNALAALA(chain B and (resid 3 through 88 or resid 90...BA110 - 111112 - 113
25LYSLYSLEULEU(chain B and (resid 3 through 88 or resid 90...BA3 - 4555 - 457
26LYSLYSLEULEU(chain B and (resid 3 through 88 or resid 90...BA3 - 4555 - 457
27LYSLYSLEULEU(chain B and (resid 3 through 88 or resid 90...BA3 - 4555 - 457
28LYSLYSLEULEU(chain B and (resid 3 through 88 or resid 90...BA3 - 4555 - 457

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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 / Mutation: F87A
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: Protein/peptide I7X-PHE-PHE


Mass: 476.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.69 %
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: BL10U2 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.89→72.18 Å / Num. obs: 78701 / % possible obs: 96.8 % / Redundancy: 2.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.041 / Rrim(I) all: 0.072 / Net I/σ(I): 11.4 / Num. measured all: 232165 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / % possible all: 96.2

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.89-1.993.10.36434980114100.8390.2470.4413.1
5.96-72.182.70.044682925330.9860.0320.05520.7

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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: 1.89→38.9 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 3870 4.92 %
Rwork0.1675 74779 -
obs0.169 78649 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.29 Å2 / Biso mean: 35.7266 Å2 / Biso min: 18.47 Å2
Refinement stepCycle: final / Resolution: 1.89→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 156 643 7871
Biso mean--30.35 41.84 -
Num. residues----893
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4364X-RAY DIFFRACTION4.346TORSIONAL
12B4364X-RAY DIFFRACTION4.346TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.910.2881470.23432629277696
1.91-1.930.25421450.22842629277496
1.93-1.960.26021400.21452652279297
1.96-1.990.31211430.21622663280695
1.99-2.010.26831490.20872622277197
2.01-2.040.23461420.20142712285496
2.04-2.080.22331170.1922616273397
2.08-2.110.22731380.18532691282997
2.11-2.150.19971300.18542664279496
2.15-2.180.21351260.1782687281397
2.18-2.230.22111290.18212645277496
2.23-2.270.24361320.17832704283697
2.27-2.320.23551410.18182662280396
2.32-2.380.2061320.1792663279597
2.38-2.440.24021200.17722648276895
2.44-2.50.25841450.18112668281396
2.5-2.570.20821330.18072662279597
2.57-2.660.2151410.17652664280596
2.66-2.750.20481310.17132695282697
2.75-2.860.21951400.1812672281297
2.86-2.990.18371540.1762657281197
2.99-3.150.21891230.17132664278796
3.15-3.350.18131450.16272694283997
3.35-3.610.19091430.15662680282397
3.61-3.970.16471560.14192675283198
3.97-4.540.14991450.1322727287298
4.54-5.720.16471550.15722721287698
5.72-38.90.20561280.16772713284196

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