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- PDB-1j9z: CYPOR-W677G -

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Basic information

Entry
Database: PDB / ID: 1j9z
TitleCYPOR-W677G
ComponentsNADPH-Cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / NADPH-Cytochrome P450 reductase
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / nitrate catabolic process / cellular organofluorine metabolic process / demethylation / nitric oxide dioxygenase NAD(P)H activity / carnitine metabolic process / flavonoid metabolic process / nitric oxide catabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation ...iron-cytochrome-c reductase activity / nitrate catabolic process / cellular organofluorine metabolic process / demethylation / nitric oxide dioxygenase NAD(P)H activity / carnitine metabolic process / flavonoid metabolic process / nitric oxide catabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / cytochrome-b5 reductase activity, acting on NAD(P)H / 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 / regulation of cholesterol metabolic process / cellular response to peptide hormone stimulus / response to dexamethasone / fatty acid oxidation / electron transport chain / response to hormone / response to nutrient / 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 / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsHubbard, P.A. / Shen, A.L. / Paschke, R. / Kasper, C.B. / Kim, J.J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: NADPH-cytochrome P450 oxidoreductase. Structural basis for hydride and electron transfer.
Authors: Hubbard, P.A. / Shen, A.L. / Paschke, R. / Kasper, C.B. / Kim, J.J.
History
DepositionMay 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 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

Downloads & links

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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)145,0738
Polymers141,1032
Non-polymers3,9716
Water3,783210
1
A: NADPH-Cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5374
Polymers70,5511
Non-polymers1,9853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-Cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5374
Polymers70,5511
Non-polymers1,9853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.634, 116.057, 118.749
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 / NADPH-Cytochrome P450 Oxidoreductase


Mass: 70551.281 Da / Num. of mol.: 2 / Mutation: W677G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CYPOR / Plasmid: pOR263 / Production host: Escherichia coli (E. coli) / Strain (production host): C1A / References: UniProt: P00388, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, Hepes, Sodium Acetate, NADP+, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 %PEG40001reservoir
2150 mMHEPES1reservoirpH7.0
3150 mM1reservoirNaAc
550 mMHEPES1droppH7.0
60.1 mMEDTA1drop
70.1 mMdithiothreitol1drop
820 mg/mlprotein1drop
4NADP+1reservoir2-fold molar excess of

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 10, 2000 / Details: Mirrors
RadiationMonochromator: Osmic blue confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 38773 / Num. obs: 30991 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 31.9 Å2 / Limit h max: 37 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 43 / Limit l min: 0 / Observed criterion F max: 219757.88 / Observed criterion F min: 0.95 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 13.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1099 / Rsym value: 0.227 / % possible all: 57.7
Reflection
*PLUS
Num. measured all: 455492
Reflection shell
*PLUS
% possible obs: 57.7 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1AMO

1amo


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1535 5 %random
Rwork0.188 ---
all-38909 --
obs-30972 79.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 10.2752 Å2 / ksol: 0.253768 e/Å3
Displacement parametersBiso max: 108.45 Å2 / Biso mean: 44.36 Å2 / Biso min: 6.63 Å2
Baniso -1Baniso -2Baniso -3
1--3.5 Å20 Å20 Å2
2---6.73 Å20 Å2
3---10.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.46 Å
Luzzati d res high-2.71
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9793 0 264 210 10267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg22.4
X-RAY DIFFRACTIONx_torsion_impr_deg2.74
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.71-2.830.29814330.30426760.0254800281958.7
2.83-2.980.2711743.60.27430160.0214800319066.5
2.98-3.170.2611843.80.26432630.0194791344771.9
3.17-3.410.2122164.40.2136590.0144864387579.7
3.41-3.750.211793.70.20139670.0164816414686.1
3.75-4.290.172044.20.16641430.0124871434789.2
4.29-5.40.1362164.40.13942800.0094910449691.6
5.4-29.80.1612194.30.1644330.0115091465291.4
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.298 / % reflection Rfree: 3 % / Rfactor Rwork: 0.304

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