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- PDB-6jvc: Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 ... -

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Basic information

Entry
Database: PDB / ID: 6jvc
TitleStructure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Monooxygenase
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 / 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
PROTOPORPHYRIN IX CONTAINING CO / Chem-WAA / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsStanfield, J.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
DepositionApr 16, 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 / pdbx_validate_chiral
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _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)109,12231
Polymers104,6012
Non-polymers4,52129
Water10,431579
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,40814
Polymers52,3011
Non-polymers2,10713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-20 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,71417
Polymers52,3011
Non-polymers2,41416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-20 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.898, 148.247, 63.219
Angle α, β, γ (deg.)90.000, 98.020, 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: 52300.660 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 , 6 types, 608 molecules

#2: 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
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→49.42 Å / Num. obs: 107592 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.049 / Rrim(I) all: 0.126 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.787.11.5291.253540.5060.6161.651100
9.59-49.426.40.049256900.9960.0210.05399.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.541
Highest resolutionLowest resolution
Rotation47.83 Å2.17 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.6.02phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WSP

3wsp


Resolution: 1.75→47.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.987 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 5319 4.9 %RANDOM
Rwork0.1857 ---
obs0.1874 102228 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.11 Å2 / Biso mean: 27.509 Å2 / Biso min: 15.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.75→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 416 579 8330
Biso mean--39.84 34.59 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138217
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177584
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.70111171
X-RAY DIFFRACTIONr_angle_other_deg1.4181.61417669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9495964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26223.521426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.045151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2341541
X-RAY DIFFRACTIONr_chiral_restr0.0910.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029136
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021681
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 399 -
Rwork0.308 7539 -
all-7938 -
obs--99.85 %

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