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- PDB-3es9: NADPH-Cytochrome P450 Reductase in an Open Conformation -

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Open data


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Basic information

Entry
Database: PDB / ID: 3es9
TitleNADPH-Cytochrome P450 Reductase in an Open Conformation
ComponentsNADPH--cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450 Reductase / Open Conformation / Acetylation / Endoplasmic reticulum / FAD / Flavoprotein / FMN / Membrane / NADP / Phosphoprotein
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHamdane, D. / Xia, C. / Im, S.-C. / Zhang, H. / Kim, J.-J. / Waskell, L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450
Authors: Hamdane, D. / Xia, C. / Im, S.C. / Zhang, H. / Kim, J.J. / Waskell, L.
History
DepositionOct 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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
B: NADPH--cytochrome P450 reductase
C: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,0929
Polymers210,7923
Non-polymers4,3006
Water0
1
A: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2494
Polymers70,2641
Non-polymers1,9853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7933
Polymers70,2641
Non-polymers1,5292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0502
Polymers70,2641
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.100, 93.000, 125.700
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 70264.062 Da / Num. of mol.: 3 / Mutation: deletion of T236G237E238E239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CYPOR, Por / Plasmid: pSC WT CPR / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P00388, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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

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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: 3 Å3/Da / Density % sol: 59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 33940 / % possible obs: 97.4 % / Biso Wilson estimate: 86 Å2

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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: PDB ENTRY 1AMO

1amo


Resolution: 3.4→29.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 43473.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1549 5 %RANDOM
Rwork0.219 ---
obs0.219 31207 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.05 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 106.2 Å2
Baniso -1Baniso -2Baniso -3
1-31.52 Å20 Å216.22 Å2
2---16.03 Å20 Å2
3----15.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 3.4→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12476 0 286 0 12762
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.312
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 177 4.3 %
Rwork0.375 3916 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2

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