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- PDB-3fjo: Structure of chimeric YH CPR -

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Basic information

Entry
Database: PDB / ID: 3fjo
TitleStructure of chimeric YH CPR
ComponentsNADPH-cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / FMN and FAD domains of CPR / Endoplasmic reticulum / Flavoprotein / Membrane / NADP / Phosphoprotein / Transmembrane / Congenital adrenal hyperplasia / Disease mutation
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / Ion homeostasis / Cytochrome P450 - arranged by substrate type / positive regulation of monooxygenase activity / cellular organofluorine metabolic process / Peroxisomal protein import / ergosterol biosynthetic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling ...Nitric oxide stimulates guanylate cyclase / Ion homeostasis / Cytochrome P450 - arranged by substrate type / positive regulation of monooxygenase activity / cellular organofluorine metabolic process / Peroxisomal protein import / ergosterol biosynthetic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / ROS and RNS production in phagocytes / NADPH dehydrogenase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / electron transport chain / xenobiotic metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / NADP binding / mitochondrial outer membrane / electron transfer activity / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / mitochondrion / membrane / plasma membrane / 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 / NADPH--cytochrome P450 reductase / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMorera, S. / Aigrain, L. / Truan, G.
CitationJournal: Embo Rep. / Year: 2009
Title: Structure of the open conformation of a functional chimeric NADPH cytochrome P450 reductase
Authors: Aigrain, L. / Pompon, D. / Morera, S. / Truan, G.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 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

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Assembly

Deposited unit
A: NADPH-cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6613
Polymers71,4191
Non-polymers1,2422
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.800, 60.700, 78.860
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 71419.328 Da / Num. of mol.: 1
Fragment: yeast FMN domain, UNP residues 44-211, human FAD domain CPR, UNP residues 232-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Homo sapiens (human)
Gene: NCP1, POR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P16603, UniProt: P16435, 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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEGII from Nextal condition G11, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2008
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 23764 / Num. obs: 23129 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.104 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 3583 / Rsym value: 0.509 / % possible all: 94.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMO (FAD domain), 2BF4 (FMN domain)

1amo

2bf4


Resolution: 2.5→19.86 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.868 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.879 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28994 1156 5 %RANDOM
Rwork0.22212 ---
obs0.22549 21958 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 0 84 123 4976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224960
X-RAY DIFFRACTIONr_bond_other_d0.0010.023315
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.986732
X-RAY DIFFRACTIONr_angle_other_deg0.8138069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15824.286238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19715829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5891531
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
X-RAY DIFFRACTIONr_nbd_refined0.2010.21097
X-RAY DIFFRACTIONr_nbd_other0.1820.23511
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22401
X-RAY DIFFRACTIONr_nbtor_other0.0850.22678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.211
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 85 -
Rwork0.288 1601 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -5.05 Å / Origin y: 3.253 Å / Origin z: 31.1874 Å
111213212223313233
T-0.0703 Å2-0.0626 Å20.0258 Å2--0.0534 Å20.0392 Å2---0.0283 Å2
L0.7623 °2-0.4787 °20.7972 °2-0.3745 °2-0.3987 °2--0.9746 °2
S-0.0108 Å °0.078 Å °0.0149 Å °-0.0117 Å °-0.0078 Å °-0.017 Å °-0.0271 Å °0.1555 Å °0.0186 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 208
2X-RAY DIFFRACTION1A209 - 225
3X-RAY DIFFRACTION1A226 - 657

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