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- PDB-1ja0: CYPOR-W677X -

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Basic information

Entry
Database: PDB / ID: 1ja0
TitleCYPOR-W677X
ComponentsNADPH-Cytochrome P450 Reductase
KeywordsOXIDOREDUCTASE / NADPH-Cytochrome P450 Reductase
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / nitrate catabolic process / organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / cytochrome-b5 reductase activity, acting on NAD(P)H ...iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / nitrate catabolic process / organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / cytochrome-b5 reductase activity, acting on NAD(P)H / nitric oxide catabolic process / positive regulation of steroid hormone biosynthetic process / positive regulation of chondrocyte differentiation / cellular response to follicle-stimulating hormone stimulus / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / cellular response to peptide hormone stimulus / fatty acid oxidation / response to dexamethasone / response to hormone / nitric oxide biosynthetic process / response to nutrient / electron transport chain / 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 / FOURIER SYNTHESIS / Resolution: 2.6 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 1.3Aug 16, 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_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)144,3297
Polymers140,8142
Non-polymers3,5145
Water4,630257
1
A: NADPH-Cytochrome P450 Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3924
Polymers70,4071
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)71,9363
Polymers70,4071
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.952, 115.527, 116.951
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: 70407.148 Da / Num. of mol.: 2
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


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#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.: 257 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 1999 / Details: mirrors
RadiationMonochromator: bent conical Si-mirror (Rh coating) + bent cylindrical Ge(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 42999 / Num. obs: 35363 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 43.2 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 44 / Limit l min: 0 / Observed criterion F max: 457287.56 / Observed criterion F min: 1.82 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 23.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4 / Num. unique all: 1412 / Rsym value: 0.155 / % possible all: 66.8
Reflection
*PLUS
Num. measured all: 305661
Reflection shell
*PLUS
% possible obs: 66.8 %

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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: 2.6→30 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1750 4.9 %random
Rwork0.209 ---
all-43068 --
obs-35355 82.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 21.9173 Å2 / ksol: 0.274683 e/Å3
Displacement parametersBiso max: 101.28 Å2 / Biso mean: 45.48 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1--10.63 Å20 Å20 Å2
2---9.56 Å20 Å2
3---20.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.36 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 233 257 8825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_torsion_deg23.4
X-RAY DIFFRACTIONx_torsion_impr_deg2.78
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 (%)
2.6-2.720.2831753.30.28833080.0215311348365.6
2.72-2.860.2562063.90.26436820.0185309388873.2
2.86-3.040.2571753.30.26140010.0195342417678.2
3.04-3.280.2472174.10.24542210.0175344443883
3.28-3.610.2272424.50.2243510.0155340459386
3.61-4.130.1842394.40.1844630.0125390470287.2
4.13-5.190.1562394.40.15647580.015422499792.2
5.19-29.720.2182574.60.21948210.0145639507890.1
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.283 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.288

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