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- PDB-8hou: Crystal structure of the P450 BM3 heme domain mutant F87A-T268V i... -

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Basic information

Entry
Database: PDB / ID: 8hou
TitleCrystal structure of the P450 BM3 heme domain mutant F87A-T268V in complex with Im-N-C4-Phe-Phe
Components
  • Bifunctional cytochrome P450/NADPH--P450 reductase
  • Im-N-C4-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 / 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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207112 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
DepositionDec 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 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 1.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Im-N-C4-Phe-Phe
D: Im-N-C4-Phe-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8846
Polymers107,6514
Non-polymers1,2332
Water19,2761070
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)58.592, 147.608, 64.764
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 53350.785 Da / Num. of mol.: 2 / Mutation: F87A, T268V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Protein/peptide Im-N-C4-Phe-Phe


Mass: 474.552 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.: 1070 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→73.8 Å / Num. obs: 106441 / % possible obs: 98.6 % / Redundancy: 2.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.044 / Rrim(I) all: 0.078 / Χ2: 0.94 / Net I/σ(I): 10 / Num. measured all: 310683
Reflection shellResolution: 1.75→1.85 Å / % possible obs: 99.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.392 / Num. measured all: 39601 / Num. unique obs: 15642 / CC1/2: 0.754 / Rpim(I) all: 0.298 / Rrim(I) all: 0.495 / Χ2: 0.7 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimlessdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→57.7 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 4998 4.7 %
Rwork0.1868 --
obs0.1878 106351 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→57.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 156 1070 8361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047479
X-RAY DIFFRACTIONf_angle_d0.73610151
X-RAY DIFFRACTIONf_dihedral_angle_d20.1812753
X-RAY DIFFRACTIONf_chiral_restr0.0461090
X-RAY DIFFRACTIONf_plane_restr0.0051318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.30641680.27693407X-RAY DIFFRACTION99
1.77-1.790.28281660.2693363X-RAY DIFFRACTION99
1.79-1.820.27351670.26113394X-RAY DIFFRACTION99
1.82-1.840.2531690.24543424X-RAY DIFFRACTION99
1.84-1.860.29141660.23133361X-RAY DIFFRACTION99
1.86-1.890.25731710.23323468X-RAY DIFFRACTION99
1.89-1.920.29351650.23353351X-RAY DIFFRACTION100
1.92-1.950.2651670.25373352X-RAY DIFFRACTION98
1.95-1.980.26211670.21373379X-RAY DIFFRACTION99
1.98-2.010.21951680.19063421X-RAY DIFFRACTION100
2.01-2.040.22481670.19023411X-RAY DIFFRACTION100
2.04-2.080.2051690.18753399X-RAY DIFFRACTION99
2.08-2.120.19411670.18633402X-RAY DIFFRACTION100
2.12-2.160.20171700.18043450X-RAY DIFFRACTION100
2.16-2.210.24271670.17723369X-RAY DIFFRACTION99
2.21-2.260.2161670.18083415X-RAY DIFFRACTION99
2.26-2.320.19421680.18053408X-RAY DIFFRACTION99
2.32-2.380.19721670.18183373X-RAY DIFFRACTION99
2.38-2.450.21411680.18383415X-RAY DIFFRACTION99
2.45-2.530.2551660.19253376X-RAY DIFFRACTION99
2.53-2.620.24151670.19783384X-RAY DIFFRACTION98
2.62-2.730.22611660.19613358X-RAY DIFFRACTION98
2.73-2.850.20561660.19313357X-RAY DIFFRACTION98
2.85-30.22841650.19353340X-RAY DIFFRACTION98
3-3.190.21741640.18553335X-RAY DIFFRACTION97
3.19-3.430.16981650.18143341X-RAY DIFFRACTION96
3.43-3.780.21081630.16633309X-RAY DIFFRACTION96
3.78-4.330.16551620.15843298X-RAY DIFFRACTION96
4.33-5.450.16891630.16033289X-RAY DIFFRACTION95
5.45-57.70.1951670.19093404X-RAY DIFFRACTION97

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