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- PDB-6t1t: Cytochrome P450 reductase in complex with NADPH from Candida trop... -

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Basic information

Entry
Database: PDB / ID: 6t1t
TitleCytochrome P450 reductase in complex with NADPH from Candida tropicalis
ComponentsNADPH--cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450 reductase / CPR
Function / homology
Function and homology information


ergosterol biosynthetic process / NADPH dehydrogenase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / FMN binding / flavin adenine dinucleotide binding / NADP binding / mitochondrial outer membrane / electron transfer activity / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
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 ...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 / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Chem-NDP / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsOpperman, D.J. / Sewell, B.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: Sci Rep / Year: 2019
Title: Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis.
Authors: Ebrecht, A.C. / van der Bergh, N. / Harrison, S.T.L. / Smit, M.S. / Sewell, B.T. / Opperman, D.J.
History
DepositionOct 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,7488
Polymers153,7742
Non-polymers3,9756
Water6,684371
1
A: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8744
Polymers76,8871
Non-polymers1,9873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8744
Polymers76,8871
Non-polymers1,9873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.657, 67.497, 143.994
Angle α, β, γ (deg.)90.000, 91.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NADPH--cytochrome P450 reductase / P450R


Mass: 76886.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: CPR-b, NCP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5PXH3, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5 / Details: 0.2 M Sodium malonate pH 5.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.08→143.94 Å / Num. obs: 82779 / % possible obs: 96.1 % / Redundancy: 3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.127 / Rrim(I) all: 0.231 / Net I/σ(I): 4 / Num. measured all: 252423 / Scaling rejects: 21
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.943 / Num. unique obs: 11409 / CC1/2: 0.394 / Rpim(I) all: 1.286 / Rrim(I) all: 2.339 / % possible all: 91.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BN4

2bn4


Resolution: 2.08→74.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2562 / WRfactor Rwork: 0.2029 / FOM work R set: 0.6421 / SU B: 11.637 / SU ML: 0.261 / SU R Cruickshank DPI: 0.2613 / SU Rfree: 0.2134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 4041 4.9 %RANDOM
Rwork0.2191 ---
obs0.2215 78196 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.3 Å2 / Biso mean: 38.278 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.05 Å2
2---0.02 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.08→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10178 0 230 371 10779
Biso mean--34.18 38.85 -
Num. residues----1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179548
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.65914476
X-RAY DIFFRACTIONr_angle_other_deg1.2621.58422224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23151272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55323.116584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.662151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2931560
X-RAY DIFFRACTIONr_chiral_restr0.0620.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022248
LS refinement shellResolution: 2.082→2.136 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 284 -
Rwork0.423 5214 -
all-5498 -
obs--86.39 %

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