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- PDB-6jzs: Structure of the Manganese Protoporphyrin IX-Reconstituted CYP102... -

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Basic information

Entry
Database: PDB / ID: 6jzs
TitleStructure of the Manganese Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan in complex with Pyridine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Monooxygenase
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 / Cytochrome p450 / Cytochrome P450 / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...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 / Cytochrome p450 / Cytochrome P450 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
pyridine / MANGANESE PROTOPORPHYRIN IX / Chem-WAA / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsStanfield, J.K. / Omura, K. / Matsumoto, A. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR15P3 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain.
Authors: Stanfield, J.K. / Omura, K. / Matsumoto, A. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O.
History
DepositionMay 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,32213
Polymers112,5082
Non-polymers2,81411
Water9,476526
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5295
Polymers56,2541
Non-polymers1,2754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-20 kcal/mol
Surface area18890 Å2
MethodPISA
2
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7938
Polymers56,2541
Non-polymers1,5397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-20 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.715, 146.129, 62.481
Angle α, β, γ (deg.)90.000, 96.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 56253.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 5 types, 537 molecules

#2: Chemical ChemComp-0PY / pyridine / Azabenzene / Azine


Mass: 79.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N
#3: Chemical ChemComp-WAA / (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid / N-Abietoyl-L-Tryptophan


Mass: 488.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H40N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MNH / MANGANESE PROTOPORPHYRIN IX


Mass: 615.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32MnN4O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 125 uM N-Abietoyl-L-Tryptophan, 100 uM Pyridine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→47.33 Å / Num. obs: 118187 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.68-1.715.41.4271.156700.5270.6691.5897.3
9.2-47.295.90.069227380.9950.030.07698.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.56
Highest resolutionLowest resolution
Rotation47.29 Å1.99 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.6.04phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WSP

3wsp


Resolution: 1.68→47.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.84 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 5867 5 %RANDOM
Rwork0.18 ---
obs0.1814 112258 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.72 Å2 / Biso mean: 27.758 Å2 / Biso min: 15.61 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.68→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7310 0 200 526 8036
Biso mean--32.06 33.35 -
Num. residues----906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137935
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177326
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.68510800
X-RAY DIFFRACTIONr_angle_other_deg1.3591.60817085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46123.539421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.089151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7521540
X-RAY DIFFRACTIONr_chiral_restr0.0820.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028934
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021643
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 422 -
Rwork0.326 8098 -
all-8520 -
obs--97.39 %

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