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- PDB-7l18: Crystal structure of a tandem deletion mutant of rat NADPH-cytoch... -

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Basic information

Entry
Database: PDB / ID: 7l18
TitleCrystal structure of a tandem deletion mutant of rat NADPH-cytochrome P450 reductase
ComponentsNADPH--cytochrome P450 reductase
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / Catalytic mechanism / Hydride transfer
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / nitrate catabolic process / cellular 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 / nitric oxide catabolic process ...iron-cytochrome-c reductase activity / nitrate catabolic process / cellular 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 / nitric oxide catabolic process / 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 / cellular response to peptide hormone stimulus / regulation of cholesterol metabolic process / response to dexamethasone / fatty acid oxidation / response to nutrient / response to hormone / electron transport chain / FMN binding / NADP binding / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer 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 / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.542 Å
AuthorsHubbard, P.A. / Xia, C. / Shen, A.L. / Kim, J.J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM097031 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Structural and kinetic investigations of the carboxy terminus of NADPH-cytochrome P450 oxidoreductase.
Authors: Hubbard, P.A. / Xia, C. / Shen, A.L. / Kim, J.P.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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
AAA: NADPH--cytochrome P450 reductase
BBB: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,9038
Polymers140,9322
Non-polymers3,9716
Water5,765320
1
AAA: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4524
Polymers70,4661
Non-polymers1,9853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4524
Polymers70,4661
Non-polymers1,9853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.058, 114.821, 120.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 70466.219 Da / Num. of mol.: 2 / Fragment: UNP residues 57-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Por / Variant: DELTA56 / Plasmid: pOR263 / Production host: Escherichia coli (E. coli) / Strain (production host): C-1A / References: UniProt: P00388, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.52 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG4000, 150 mM HEPES, pH 7.0, 150 mM sodium acetate, protein, two-fold molar excess of NADP+

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 22, 1999
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→30 Å / Num. obs: 43215 / % possible obs: 91.9 % / Redundancy: 3 % / Rsym value: 0.09 / Net I/σ(I): 16.7
Reflection shellResolution: 2.54→2.59 Å / Rmerge(I) obs: 0.263 / Num. unique obs: 1879

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1AMO

1amo


Resolution: 2.542→29.787 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.185 / SU B: 11.843 / SU ML: 0.247 / Average fsc free: 0.8899 / Average fsc work: 0.9144 / Cross valid method: FREE R-VALUE / ESU R Free: 0.342
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2538 2143 5.007 %
Rwork0.1807 40657 -
all0.184 --
obs-42800 89.816 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.818 Å2-0 Å2-0 Å2
2---1.681 Å20 Å2
3---2.499 Å2
Refinement stepCycle: LAST / Resolution: 2.542→29.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9724 0 247 320 10291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01310222
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179316
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.6513879
X-RAY DIFFRACTIONr_angle_other_deg1.2221.58121476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92851205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89722.168572
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.587101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01151696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.221570
X-RAY DIFFRACTIONr_chiral_restr0.0590.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022391
X-RAY DIFFRACTIONr_nbd_refined0.2010.22045
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.28691
X-RAY DIFFRACTIONr_nbtor_refined0.1660.24718
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2351
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0890.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.212
X-RAY DIFFRACTIONr_nbd_other0.3180.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3210.21
X-RAY DIFFRACTIONr_mcbond_it3.034.9544838
X-RAY DIFFRACTIONr_mcbond_other3.0294.9534837
X-RAY DIFFRACTIONr_mcangle_it4.7497.426037
X-RAY DIFFRACTIONr_mcangle_other4.7497.4216038
X-RAY DIFFRACTIONr_scbond_it3.0545.2535384
X-RAY DIFFRACTIONr_scbond_other3.0555.2555377
X-RAY DIFFRACTIONr_scangle_it4.9817.747842
X-RAY DIFFRACTIONr_scangle_other4.987.747843
X-RAY DIFFRACTIONr_lrange_it7.66156.36611340
X-RAY DIFFRACTIONr_lrange_other7.6656.37311313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.542-2.6080.3731130.2712327X-RAY DIFFRACTION70.2967
2.608-2.6790.3091500.2472781X-RAY DIFFRACTION86.282
2.679-2.7570.3291420.2532755X-RAY DIFFRACTION88.5662
2.757-2.8420.2731460.2072744X-RAY DIFFRACTION90.2561
2.842-2.9350.2911570.2042678X-RAY DIFFRACTION91.0112
2.935-3.0380.2931350.2112651X-RAY DIFFRACTION92.3128
3.038-3.1520.2851380.2052579X-RAY DIFFRACTION93.4641
3.152-3.2810.3141270.2042475X-RAY DIFFRACTION92.4006
3.281-3.4260.2711330.1972309X-RAY DIFFRACTION91.5636
3.426-3.5930.2561350.1882229X-RAY DIFFRACTION91.2389
3.593-3.7870.2541280.1932120X-RAY DIFFRACTION91.3821
3.787-4.0170.226950.1692003X-RAY DIFFRACTION91.0195
4.017-4.2930.2091000.1471956X-RAY DIFFRACTION92.2801
4.293-4.6360.195810.1341847X-RAY DIFFRACTION94.2327
4.636-5.0770.193910.1321715X-RAY DIFFRACTION95.6568
5.077-5.6740.227910.1581580X-RAY DIFFRACTION96.4224
5.674-6.5470.242780.161418X-RAY DIFFRACTION97.4593
6.547-8.0060.249480.1421233X-RAY DIFFRACTION96.972
8.006-11.2720.163350.146871X-RAY DIFFRACTION86.7816
11.272-29.7870.314200.257384X-RAY DIFFRACTION64.127

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