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- PDB-1amo: THREE-DIMENSIONAL STRUCTURE OF NADPH-CYTOCHROME P450 REDUCTASE: P... -

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Basic information

Entry
Database: PDB / ID: 1amo
TitleTHREE-DIMENSIONAL STRUCTURE OF NADPH-CYTOCHROME P450 REDUCTASE: PROTOTYPE FOR FMN-AND FAD-CONTAINING ENZYMES
ComponentsNADPH-CYTOCHROME P450 REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NITRIC OXIDE SYNTHASE
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 / MIR / Resolution: 2.6 Å
AuthorsWang, M. / Roberts, D.L. / Paschke, R. / Shea, T.M. / Masters, B.S.S. / Kim, J.J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes.
Authors: Wang, M. / Roberts, D.L. / Paschke, R. / Shea, T.M. / Masters, B.S. / Kim, J.J.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9148
Polymers139,9432
Non-polymers3,9716
Water2,810156
1
A: NADPH-CYTOCHROME P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9574
Polymers69,9721
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)71,9574
Polymers69,9721
Non-polymers1,9853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.280, 116.180, 119.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99752, -0.00364, 0.07025), (-0.00364, -0.99466, -0.10311), (0.07025, -0.10311, 0.99219)
Vector: 49.809, 28.30732, -0.29123)

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Components

#1: Protein NADPH-CYTOCHROME P450 REDUCTASE / CPR / P450R


Mass: 69971.641 Da / Num. of mol.: 2 / Fragment: HYDROPHILIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: MITOCHONDRIAMitochondrion / Organ: LIVER / Production host: Escherichia coli (E. coli) / 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.: 156 / 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: 2.49 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 6.5 / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
221 %PEG45001reservoir
3150 mMHEPES1reservoir
45 mM1reservoirMgCl2
50.8 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 17, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 41132 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.07 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.308 / % possible all: 85.8
Reflection
*PLUS
Num. measured all: 171499 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 85.8 % / Rmerge(I) obs: 0.308

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1977 5 %RANDOM
Rwork0.2 ---
obs0.2 37046 91.5 %-
Displacement parametersBiso mean: 26.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4925 115 0 78 5118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 195 5.7 %
Rwork0.29 3421 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16
LS refinement shell
*PLUS
Rfactor obs: 0.29

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