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- PDB-7cx8: Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valero... -

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Basic information

Entry
Database: PDB / ID: 7cx8
TitleStructure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Tetralylamine
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 / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
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
(1R)-1,2,3,4-tetrahydronaphthalen-1-amine / Chem-GKX / PROTOPORPHYRIN IX CONTAINING FE / (1~{S})-1,2,3,4-tetrahydronaphthalen-1-amine / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsStanfield, J.K. / Sugimoto, H. / Shoji, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR15P3 Japan
CitationJournal: To Be Published
Title: Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Tetralylamine at 1.70 Angstrom Resolution
Authors: Shoji, O. / Stanfield, J.K.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)108,46725
Polymers104,6012
Non-polymers3,86623
Water10,142563
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A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,28013
Polymers52,3011
Non-polymers1,97912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-21 kcal/mol
Surface area18980 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,18812
Polymers52,3011
Non-polymers1,88711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-21 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.793, 128.580, 147.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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, 586 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-GKX / (2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid


Mass: 331.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1Y5 / (1R)-1,2,3,4-tetrahydronaphthalen-1-amine


Mass: 147.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-STQ / (1~{S})-1,2,3,4-tetrahydronaphthalen-1-amine


Mass: 147.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 200 uM N-(5-Cyclohexyl)valeroyl-L-phenylalanine, 1 mM (R)-1-Tetralylamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→49.28 Å / Num. obs: 123952 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.037 / Rrim(I) all: 0.141 / Net I/σ(I): 14.3 / Num. measured all: 1831100 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7314.82.8551.160840.5080.7652.957100
9.31-49.2812.60.02854.488010.0080.02999.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.49
Highest resolutionLowest resolution
Rotation48.51 Å1.93 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XA3

5xa3


Resolution: 1.7→48.56 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.824 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 6214 5 %RANDOM
Rwork0.1861 ---
obs0.1876 117643 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.04 Å2 / Biso mean: 24.459 Å2 / Biso min: 12.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--1.89 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.7→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 286 563 8191
Biso mean--31.7 31.97 -
Num. residues----910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138080
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177549
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.68310958
X-RAY DIFFRACTIONr_angle_other_deg1.3571.6117607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98523.318422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.027151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.481543
X-RAY DIFFRACTIONr_chiral_restr0.0780.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028985
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021650
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 494 -
Rwork0.365 8566 -
all-9060 -
obs--99.83 %

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