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

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Basic information

Entry
Database: PDB / ID: 7sux
TitleNADPH-dependent cytochrome P450 reductase 2b from Sorghum bicolor (SbCPR2b) -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: 2.36 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
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-8 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.127, 69.653, 153.271
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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 24.3 %
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: 2.36→37.82 Å / Num. obs: 21324 / % possible obs: 99.08 % / Redundancy: 6.9 % / Biso Wilson estimate: 57.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1129 / Net I/σ(I): 13.58
Reflection shellResolution: 2.36→2.444 Å / Rmerge(I) obs: 1.768 / Num. unique obs: 1939 / CC1/2: 0.409

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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: 2.36→37.82 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1997 9.37 %
Rwork0.2323 19306 -
obs0.2353 21303 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.23 Å2 / Biso mean: 75.8831 Å2 / Biso min: 30.77 Å2
Refinement stepCycle: final / Resolution: 2.36→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 126 40 3185
Biso mean--76.15 60.28 -
Num. residues----388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.36-2.420.37551240.36481190131488
2.42-2.480.35931430.334513801523100
2.48-2.560.33661390.320413541493100
2.56-2.640.35991420.293413671509100
2.64-2.730.32861400.294313521492100
2.73-2.840.34221430.295513791522100
2.84-2.970.3581430.311913821525100
2.97-3.130.30451440.275213911535100
3.13-3.330.29321420.276513761518100
3.33-3.580.30581440.256713901534100
3.58-3.940.241450.214914011546100
3.94-4.510.20531460.200314001546100
4.51-5.680.24751460.197314331579100
5.68-37.820.21831560.18651511166799
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)
15.52272.5729-1.44843.81720.04483.77470.0166-0.1854-0.11790.67310.4043-0.0644-0.13620.2641-0.41690.72340.1082-0.14890.52890.07780.604861.215139.48130.071
21.6045-0.65251.18442.2558-1.45436.39310.1047-0.2521-0.14340.2485-0.0118-0.18710.1930.2742-0.10310.3103-0.0442-0.01290.32020.06240.477252.597146.90217.904
33.9198-1.4906-1.58134.76131.21984.3011-0.1924-1.1928-0.07591.37810.19330.01970.74240.62710.00741.0221-0.0399-0.05110.761-0.00150.459850.522145.5850.847
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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