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- PDB-5jqv: Crystal structure of Cytochrome P450 BM3 heme domain T269V/L272W/... -

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Basic information

Entry
Database: PDB / ID: 5jqv
TitleCrystal structure of Cytochrome P450 BM3 heme domain T269V/L272W/L322I/A406S (WIVS) variant with iron(III) deuteroporphyrin IX bound
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / P450 BM3 / iron(III) deuteroporphyrin IX
Function / homology
Function and homology information


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 / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...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 / aromatase activity / metabolic process / response to hormone / 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 / Cytochrome p450 / Cytochrome P450 / 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. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FE(III) DEUTEROPORPHYRIN IX / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsReynolds, E.W. / McHenry, M.W. / Cannac, F. / Gober, J.G. / Snow, C.D. / Brustad, E.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Defense Advanced Research Projects AgencyD13AP00024 United States
National Science Foundation (NSF, United States)DGE1144081 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: An Evolved Orthogonal Enzyme/Cofactor Pair.
Authors: Reynolds, E.W. / McHenry, M.W. / Cannac, F. / Gober, J.G. / Snow, C.D. / Brustad, E.M.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
E: Bifunctional cytochrome P450/NADPH--P450 reductase
F: Bifunctional cytochrome P450/NADPH--P450 reductase
G: Bifunctional cytochrome P450/NADPH--P450 reductase
H: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,71116
Polymers432,1958
Non-polymers4,5158
Water20,9511163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19480 Å2
ΔGint-180 kcal/mol
Surface area141590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.708, 167.405, 228.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 4:8 OR (RESID 9 AND (NAME...
211(CHAIN B AND ((RESID 4 AND (NAME N OR NAME...
311(CHAIN C AND (RESSEQ 4:12 OR (RESID 14 AND (NAME...
411(CHAIN D AND ((RESID 4 AND (NAME N OR NAME...
511(CHAIN E AND ((RESID 4 AND (NAME N OR NAME...
611(CHAIN F AND ((RESID 4 AND (NAME N OR NAME...
711(CHAIN G AND (RESSEQ 4:12 OR (RESID 14 AND (NAME...
811(CHAIN H AND ((RESID 4 AND (NAME N OR NAME...

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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: 54024.430 Da / Num. of mol.: 8 / Fragment: heme domain, residues 2-456 / Mutation: T269V,L272W,L322I,A406S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512) (bacteria)
Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512
Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-FDE / FE(III) DEUTEROPORPHYRIN IX


Mass: 564.413 Da / Num. of mol.: 8 / Fragment: iron(III) deuteroporphyrin IX / Source method: obtained synthetically / Formula: C30H28FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.25 M MgCl2, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.336→32.97 Å / Num. obs: 173212 / % possible obs: 99.9 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 9
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQU

5jqu


Resolution: 2.34→32.97 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.62 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.284 1628 0.94 %
Rwork0.215 --
obs0.215 173212 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.7 Å2
Refinement stepCycle: LAST / Resolution: 2.34→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28514 0 312 1163 29989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929607
X-RAY DIFFRACTIONf_angle_d1.14940265
X-RAY DIFFRACTIONf_dihedral_angle_d16.67817799
X-RAY DIFFRACTIONf_chiral_restr0.0614364
X-RAY DIFFRACTIONf_plane_restr0.0085224
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A14701X-RAY DIFFRACTIONPOSITIONAL
12B14701X-RAY DIFFRACTIONPOSITIONAL
13C14701X-RAY DIFFRACTIONPOSITIONAL
14D14701X-RAY DIFFRACTIONPOSITIONAL
15E14701X-RAY DIFFRACTIONPOSITIONAL
16F14701X-RAY DIFFRACTIONPOSITIONAL
17G14701X-RAY DIFFRACTIONPOSITIONAL
18H14701X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3361-2.40480.39381280.355214166X-RAY DIFFRACTION100
2.4048-2.48240.36561420.316114219X-RAY DIFFRACTION100
2.4824-2.57110.35561460.288614099X-RAY DIFFRACTION100
2.5711-2.6740.34941220.274914215X-RAY DIFFRACTION100
2.674-2.79560.34821290.256914231X-RAY DIFFRACTION100
2.7956-2.9430.33291380.237814177X-RAY DIFFRACTION100
2.943-3.12720.28671390.222314240X-RAY DIFFRACTION100
3.1272-3.36840.2971330.210614301X-RAY DIFFRACTION100
3.3684-3.7070.28671370.193114284X-RAY DIFFRACTION100
3.707-4.24250.23191390.16914370X-RAY DIFFRACTION100
4.2425-5.34140.2171360.149514470X-RAY DIFFRACTION100
5.3414-32.96830.21081390.157614812X-RAY DIFFRACTION100

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