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- PDB-7coo: Structure of the CYP102A1 Haem Domain with N-Carboxybenzyl-L-Prol... -

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Basic information

Entry
Database: PDB / ID: 7coo
TitleStructure of the CYP102A1 Haem Domain with N-Carboxybenzyl-L-Prolyl-L-Phenylalanine in complex with Cyclohexylamine
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 / 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
CYCLOHEXYLAMMONIUM ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-ZP6 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 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-Carboxybenzyl-L-Prolyl-L-Phenylalanine in complex with Cyclohexylamine at 1.49 Angstrom Resolution
Authors: Shoji, O. / Stanfield, J.K.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 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)107,47215
Polymers104,6012
Non-polymers2,87113
Water16,033890
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8749
Polymers52,3011
Non-polymers1,5748
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5986
Polymers52,3011
Non-polymers1,2975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.820, 128.830, 149.330
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 , 5 types, 903 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N
#4: Chemical ChemComp-ZP6 / (2S)-3-phenyl-2-[[(2S)-1-phenylmethoxycarbonylpyrrolidin-2-yl]carbonylamino]propanoic acid


Mass: 396.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 200 uM N-Carboxybenzyl-L-Prolyl-L-Phenylalanine, 500 uM Cyclohexylamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→48.82 Å / Num. obs: 176109 / % possible obs: 100 % / Redundancy: 11.415 % / Biso Wilson estimate: 27.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.116 / Χ2: 1.18 / Net I/σ(I): 10.78 / Num. measured all: 4088508 / Scaling rejects: 3950
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.49-1.5311.6442.31130855326501265000.522.416100
1.53-1.5711.5721.7751.3429934125870258680.6591.858100
1.57-1.6211.4321.381.7728714025118251170.7821.445100
1.62-1.6711.0891.1452.1627031624378243770.8351.201100
1.67-1.7210.5030.8872.7224886223695236950.8810.933100
1.72-1.7811.0130.7013.5925210622891228910.9340.735100
1.78-1.8511.8220.5394.8726044322033220300.9620.564100
1.85-1.9212.2270.4096.4625935121214212120.980.426100
1.92-2.0112.1820.3068.5224821220377203750.9880.32100
2.01-2.1112.120.23410.9123645919510195100.9930.245100
2.11-2.2211.9830.18113.622119118459184590.9950.189100
2.22-2.3611.8360.14516.0720815817589175870.9970.152100
2.36-2.5211.5710.12118.2418949216377163770.9970.127100
2.52-2.7211.0520.10120.5416934815323153230.9980.106100
2.72-2.989.8610.08622.5413911214108141080.9980.091100
2.98-3.3310.0270.07126.4912750512716127160.9980.075100
3.33-3.8510.9330.05932.412274411227112270.9990.062100
3.85-4.7111.2870.05136107321950895080.9990.053100
4.71-6.6611.7670.04636.1286019731073100.9990.048100
6.66-48.8211.750.03538.12468354002398610.03699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.48
Highest resolutionLowest resolution
Rotation46.41 Å1.93 Å

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Processing

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

5xa3


Resolution: 1.49→48.82 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.728 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 9220 5 %RANDOM
Rwork0.139 ---
obs0.1409 176109 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: 83.79 Å2 / Biso mean: 23.457 Å2 / Biso min: 12.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.49→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7328 0 286 890 8504
Biso mean--26.43 35.19 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138100
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177488
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.69511047
X-RAY DIFFRACTIONr_angle_other_deg1.4411.60717460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12523.507422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.096151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1181541
X-RAY DIFFRACTIONr_chiral_restr0.0840.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029134
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021683
X-RAY DIFFRACTIONr_rigid_bond_restr1.795315588
LS refinement shellResolution: 1.49→1.529 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 638 -
Rwork0.303 12911 -
all-13549 -
obs--99.9 %

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