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- PDB-1ja1: CYPOR-Triple Mutant -

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Basic information

Entry
Database: PDB / ID: 1ja1
TitleCYPOR-Triple Mutant
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 / positive regulation of steroid hormone biosynthetic process / nitrate catabolic process / demethylation / organofluorine metabolic process / carnitine metabolic process / flavonoid metabolic process / cellular response to gonadotropin stimulus / nitric oxide dioxygenase NAD(P)H activity ...iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / positive regulation of steroid hormone biosynthetic process / nitrate catabolic process / demethylation / organofluorine metabolic process / carnitine metabolic process / flavonoid metabolic process / cellular response to gonadotropin stimulus / nitric oxide dioxygenase NAD(P)H activity / cytochrome-b5 reductase activity, acting on NAD(P)H / nitric oxide catabolic 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 / response to dexamethasone / fatty acid oxidation / 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: 1.8 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)145,4729
Polymers141,2632
Non-polymers4,2097
Water20,2851126
1
A: NADPH-Cytochrome P450 Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6174
Polymers70,6311
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)72,8555
Polymers70,6311
Non-polymers2,2244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.437, 115.159, 118.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NADPH-Cytochrome P450 Reductase / NADPH-Cytochrome P450 Oxidoreductase


Mass: 70631.391 Da / Num. of mol.: 2 / Mutation: S457A/C630A/D675N
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

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Non-polymers , 5 types, 1133 molecules

#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.: 2 / 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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1126 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
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: Nov 21, 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: 1.8→30 Å / Num. all: 129222 / Num. obs: 120472 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 15.6 Å2 / Limit h max: 56 / Limit h min: 0 / Limit k max: 64 / Limit k min: 0 / Limit l max: 65 / Limit l min: 0 / Observed criterion F max: 473892.21 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 34.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4536 / Rsym value: 0.285 / % possible all: 70.8
Reflection
*PLUS
Num. measured all: 1504516
Reflection shell
*PLUS
% possible obs: 70.8 %

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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: 1.8→29.16 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 6070 5.1 %random
Rwork0.208 ---
all-128789 --
obs-120162 93.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 42.1015 Å2 / ksol: 0.330899 e/Å3
Displacement parametersBiso max: 100.1 Å2 / Biso mean: 34.95 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å20 Å20 Å2
2---4.37 Å20 Å2
3---7.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9846 0 279 1126 11251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg22.8
X-RAY DIFFRACTIONx_torsion_impr_deg3.14
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 (%)
1.8-1.880.3385813.60.338114110.014160051199274.9
1.88-1.980.2927184.50.292135120.011159391423089.3
1.98-2.110.2377354.60.237142540.009160111498993.6
2.11-2.270.2257744.80.226143800.008159951515494.7
2.27-2.50.2127864.90.212145990.008160341538596
2.5-2.860.20480950.204150800.007161061588998.6
2.86-3.60.1978365.20.197152800.007162291611699.3
3.6-29.160.17383150.173155760.006166241640798.7
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.338 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.338

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