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

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Basic information

Entry
Database: PDB / ID: 7suz
TitleNADPH-dependent cytochrome P450 reductase 2b from Sorghum bicolor (SbCPR2b)
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 / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)78,3392
Polymers77,5531
Non-polymers7861
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.143, 68.894, 154.265
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.62 Å3/Da / Density % sol: 23.98 %
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: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18089 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 56.54 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.012 / Net I/σ(I): 7.8 / Num. measured all: 128366
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.91.1358820.7240.4591.2260.86699.8
2.54-2.597.20.9428940.760.3751.0150.942100
2.59-2.647.20.8618800.8950.3420.9270.88399.9
2.64-2.697.20.6878720.8410.2730.740.96599.8
2.69-2.757.30.5719100.9020.2270.6150.96499.9
2.75-2.827.30.4918590.9290.1950.5291.004100
2.82-2.897.20.3718900.9590.1480.41.066100
2.89-2.967.20.339080.9640.1310.3561.085100
2.96-3.057.30.2658560.9730.1050.2861.103100
3.05-3.157.20.1989210.9820.0790.2141.068100
3.15-3.267.30.1728810.9880.0690.1861.089100
3.26-3.397.20.1239120.9930.0490.1331.024100
3.39-3.557.20.1018950.9950.0410.1091.058100
3.55-3.737.10.0848980.9960.0340.0911.023100
3.73-3.977.10.0819190.9950.0330.0871.063100
3.97-4.277.10.0729100.9970.0290.0780.996100
4.27-4.76.90.0599160.9970.0240.0641.04100
4.7-5.386.80.0519170.9970.0220.0560.998100
5.38-6.786.80.0469520.9980.0190.051.037100
6.78-506.50.05610170.9950.0240.0610.95299.6

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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: 2.5→45.08 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 1804 10 %
Rwork0.209 16228 -
obs0.2126 18032 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.65 Å2 / Biso mean: 64.2349 Å2 / Biso min: 26.97 Å2
Refinement stepCycle: final / Resolution: 2.5→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 84 100 3210
Biso mean--49.06 49.22 -
Num. residues----389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.570.42851330.39061195132898
2.57-2.640.4211380.335412401378100
2.64-2.730.29411340.279912071341100
2.73-2.830.33211370.24212411378100
2.83-2.940.27421380.222612291367100
2.94-3.070.27231360.237612391375100
3.07-3.240.29431380.244412341372100
3.24-3.440.2571390.245912491388100
3.44-3.70.25521350.206312181353100
3.7-4.080.22421410.191512681409100
4.08-4.670.20341400.173512641404100
4.67-5.880.22961430.187412871430100
5.88-45.080.2011520.178913571509100

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