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- PDB-3ojx: Disulfide crosslinked cytochrome P450 reductase inactive -

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Basic information

Entry
Database: PDB / ID: 3ojx
TitleDisulfide crosslinked cytochrome P450 reductase inactive
ComponentsNADPH-Cytochrome P450 Reductase
KeywordsOXIDOREDUCTASE / cytochrome P450 reductase / CYPOR / Disulfide crosslinked / inactive
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / nitrate catabolic process / organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / cytochrome-b5 reductase activity, acting on NAD(P)H ...iron-cytochrome-c reductase activity / nitrate catabolic process / organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / cytochrome-b5 reductase activity, acting on NAD(P)H / nitric oxide catabolic process / positive regulation of steroid hormone biosynthetic process / positive regulation of chondrocyte differentiation / cellular response to follicle-stimulating hormone stimulus / positive regulation of cholesterol biosynthetic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / cellular response to peptide hormone stimulus / regulation of cholesterol metabolic process / response to dexamethasone / fatty acid oxidation / response to hormone / response to nutrient / electron transport chain / FMN binding / flavin adenine dinucleotide binding / NADP binding / electron transfer activity / oxidoreductase activity / hydrolase activity / response to xenobiotic stimulus / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cytosol
Similarity search - Function
NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome P450 reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Flavodoxin domain / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like ...NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome P450 reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Flavodoxin domain / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXia, C. / Hamdane, D. / Shen, A. / Choi, V. / Kasper, C. / Zhang, H. / Im, S.-C. / Waskell, L. / Kim, J.-J.P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Conformational Changes of NADPH-Cytochrome P450 Oxidoreductase Are Essential for Catalysis and Cofactor Binding.
Authors: Xia, C. / Hamdane, D. / Shen, A.L. / Choi, V. / Kasper, C.B. / Pearl, N.M. / Zhang, H. / Im, S.C. / Waskell, L. / Kim, J.J.
History
DepositionAug 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-Cytochrome P450 Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5094
Polymers70,5241
Non-polymers1,9853
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.412, 73.265, 137.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADPH-Cytochrome P450 Reductase / CPR / P450R


Mass: 70524.188 Da / Num. of mol.: 1 / Fragment: N-terminal deletion, UNP residues 57-678
Mutation: C136A, D147C, C228A, C363T, C445L, C472T, R514C, C566A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CYPOR, Por / Plasmid: pET23b-ck377 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami(DE3) pLysS / References: UniProt: P00388, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM HEPES, pH 7.2, 150 mM MgCl2 and 17% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 292KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23362 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 16.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMO

1amo


Resolution: 2.5→21.54 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 85515.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1061 4.9 %RANDOM
Rwork0.209 ---
obs0.209 21778 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.093 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-13.04 Å20 Å20 Å2
2---13.71 Å20 Å2
3---0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-30 Å
Luzzati sigma a0.45 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→21.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 132 70 5057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.792.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 142 4.4 %
Rwork0.295 3094 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cofac_1jacofac_1ja
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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