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- PDB-6k24: Structure of the Rhodium Mesoporphyrin IX-Reconstituted CYP102A1 ... -

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Basic information

Entry
Database: PDB / ID: 6k24
TitleStructure of the Rhodium Mesoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan
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 / 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 / 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
MESOPORPHYRIN IX CONTAINING Rh / Chem-WAA / Bifunctional cytochrome P450/NADPH--P450 reductase / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
DepositionMay 13, 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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,4288
Polymers109,9592
Non-polymers2,4696
Water5,368298
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2144
Polymers54,9801
Non-polymers1,2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area19110 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2144
Polymers54,9801
Non-polymers1,2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.082, 149.182, 65.213
Angle α, β, γ (deg.)90.000, 99.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 54979.508 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: F2Q7T0, UniProt: P14779*PLUS, unspecific monooxygenase, NADPH-hemoprotein reductase
#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
#3: Chemical ChemComp-CV0 / MESOPORPHYRIN IX CONTAINING Rh


Mass: 667.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36N4O4Rh
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 125uM 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: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.74 Å / Num. obs: 60178 / % possible obs: 92.9 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.043 / Rrim(I) all: 0.112 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1 / % possible all: 99.2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.1-2.156.61.091247550.6980.4531.184
9.39-48.695.40.0723.27450.9750.0340.079

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3wsp


Resolution: 2.1→48.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.555 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.21
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 2962 4.9 %RANDOM
Rwork0.2083 ---
obs0.2107 57075 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.15 Å2 / Biso mean: 43.929 Å2 / Biso min: 21.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.1→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7334 0 166 298 7798
Biso mean--42.32 43.69 -
Num. residues----910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137917
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177352
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6810763
X-RAY DIFFRACTIONr_angle_other_deg1.2721.60617143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32723.452420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.017151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7341541
X-RAY DIFFRACTIONr_chiral_restr0.0770.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021613
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 230 -
Rwork0.346 4513 -
all-4743 -
obs--99.08 %

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