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- PDB-7sv0: NADPH-dependent cytochrome P450 reductase 2b from Sorghum bicolor... -

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Basic information

Entry
Database: PDB / ID: 7sv0
TitleNADPH-dependent cytochrome P450 reductase 2b from Sorghum bicolor (SbCPR2b) -oxidized form of NADP+ complex
ComponentsNADPH--cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / NADPH-dependent cytochrome P450 reductase 2b from sorghum bicolor
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / FMN binding / flavin adenine dinucleotide binding / NADP binding / endoplasmic reticulum membrane / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, B. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1804699 United States
National Science Foundation (NSF, United States)MCB-2043248 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition.
Authors: Zhang, B. / Munske, G.R. / Timokhin, V.I. / Ralph, J. / Davydov, D.R. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0823
Polymers77,5531
Non-polymers1,5292
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-6 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.947, 69.158, 150.949
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 / CPR / P450R / SbCPR


Mass: 77553.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: CPR, SORBI_3007G088000 / Production host: Escherichia coli (E. coli) / References: UniProt: C5YJG8, NADPH-hemoprotein reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.58 Å3/Da / Density % sol: 22.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium thiocyanate, pH 6.9, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→44.83 Å / Num. obs: 14106 / % possible obs: 99.82 % / Redundancy: 5.5 % / Biso Wilson estimate: 71.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.18
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 1.537 / Num. unique obs: 1372 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5GXU

5gxu


Resolution: 2.7→44.83 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 1411 10.01 %
Rwork0.2205 12691 -
obs0.2249 14102 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.02 Å2 / Biso mean: 86.4804 Å2 / Biso min: 39.67 Å2
Refinement stepCycle: final / Resolution: 2.7→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 157 17 3200
Biso mean--89.24 58.2 -
Num. residues----389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.80.34051380.305912331371
2.8-2.910.33231390.286512541393
2.91-3.040.32861360.280212271363
3.04-3.20.29991390.264412541393
3.2-3.40.34281400.263512471387
3.4-3.660.28821400.23212671407
3.66-4.030.25921400.206612611401
4.03-4.620.22981420.190312801422
4.62-5.810.29271450.215312961441
5.82-44.830.21481520.198513721524
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.256.6769-3.99766.5755-5.64819.73570.68910.2194-0.56361.6494-0.2725-0.5133-0.42640.7371-0.44770.7670.1251-0.1190.3861-0.09220.704361.874137.90730.143
20.5307-0.23911.59352.1894-0.91427.88910.1887-0.02430.01750.08840.0365-0.1230.42130.2042-0.18980.2963-0.0261-0.02030.46470.1370.724452.918145.45617.785
35.2029-1.2373-0.4657.3263-0.00235.376-0.2173-1.2056-0.27861.9742-0.01890.53370.73330.160.28271.2371-0.0820.10670.73440.03660.579950.19143.59750.507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 300:326 )A300 - 326
2X-RAY DIFFRACTION2( CHAIN A AND RESID 327:547 )A327 - 547
3X-RAY DIFFRACTION3( CHAIN A AND RESID 548:706 )A548 - 706

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