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- PDB-6l8j: Crystal structure of CYP97A3 mutant S290D/W300L/S304V in complex ... -

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Basic information

Entry
Database: PDB / ID: 6l8j
TitleCrystal structure of CYP97A3 mutant S290D/W300L/S304V in complex with retinal
ComponentsProtein LUTEIN DEFICIENT 5, chloroplastic
KeywordsOXIDOREDUCTASE / lutein biosynthesis / photosynthesis / monooxygenase / carotenoid / P450
Function / homology
Function and homology information


carotene beta-ring hydroxylase activity / xanthophyll biosynthetic process / carotenoid biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast envelope / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / RETINAL / Protein LUTEIN DEFICIENT 5, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsNiu, G. / Guo, Q. / Liu, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for plant lutein biosynthesis from alpha-carotene.
Authors: Niu, G. / Guo, Q. / Wang, J. / Zhao, S. / He, Y. / Liu, L.
History
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein LUTEIN DEFICIENT 5, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3323
Polymers58,4311
Non-polymers9012
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-25 kcal/mol
Surface area18580 Å2
Unit cell
Length a, b, c (Å)58.182, 82.147, 110.549
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 Protein LUTEIN DEFICIENT 5, chloroplastic / Cytochrome P450 97A3


Mass: 58430.836 Da / Num. of mol.: 1 / Mutation: S290D,W300L,S304V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP97A3, LUT5, At1g31800, F5M6.19 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93VK5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: potassium sulfate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 21298 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 0.933 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.054 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.3 % / Num. unique obs: 2077 / CC1/2: 0.793 / Rpim(I) all: 0.347 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF2

4kf2


Resolution: 2.399→43.626 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2506 1087 5.12 %
Rwork0.2001 --
obs0.2025 21241 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.02 Å2 / Biso mean: 43.7637 Å2 / Biso min: 33.24 Å2
Refinement stepCycle: final / Resolution: 2.399→43.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 64 176 3683
Biso mean--37.43 44.02 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043602
X-RAY DIFFRACTIONf_angle_d0.7024913
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.004624
X-RAY DIFFRACTIONf_dihedral_angle_d12.612150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3991-2.50830.33711470.2871246399
2.5083-2.64050.31251340.2746248099
2.6405-2.8060.34631290.25372476100
2.806-3.02260.30611410.24212492100
3.0226-3.32660.24391370.2225250899
3.3266-3.80780.25211500.19432510100
3.8078-4.79640.18921090.1544258599
4.7964-43.6260.20881400.1726264098

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