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- PDB-6j95: Crystal structure of CYP97A3 in complex with retinal -

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Basic information

Entry
Database: PDB / ID: 6j95
TitleCrystal structure of CYP97A3 in complex with retinal
ComponentsProtein LUTEIN DEFICIENT 5, chloroplastic
KeywordsOXIDOREDUCTASE / lutein biosynthesis / photosynthesis / monooxygenase / carotenoid / P450
Function / homology
Function and homology information


beta-carotene 3-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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
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: 2.002 Å
AuthorsNiu, G. / Guo, Q. / Wang, J. / Zhao, S.
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
DepositionJan 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 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)59,3653
Polymers58,4641
Non-polymers9012
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-24 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.481, 82.097, 110.339
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: 58463.828 Da / Num. of mol.: 1
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
#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.: 516 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 289 K / Method: liquid diffusion / Details: 0.2 M potassium sulfate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / 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→50 Å / Num. obs: 36341 / % possible obs: 99.5 % / Redundancy: 11.1 % / Biso Wilson estimate: 29.16 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Net I/σ(I): 23.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3557 / CC1/2: 0.875 / Rpim(I) all: 0.223 / Rrim(I) all: 0.734 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF2

4kf2


Resolution: 2.002→47.632 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.29
RfactorNum. reflection% reflection
Rfree0.1972 1815 5.01 %
Rwork0.1653 --
obs0.167 36262 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.16 Å2 / Biso mean: 34.3516 Å2 / Biso min: 15.68 Å2
Refinement stepCycle: final / Resolution: 2.002→47.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 64 516 4052
Biso mean--23.92 47.02 -
Num. residues----445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043640
X-RAY DIFFRACTIONf_angle_d0.8174968
X-RAY DIFFRACTIONf_chiral_restr0.042559
X-RAY DIFFRACTIONf_plane_restr0.004634
X-RAY DIFFRACTIONf_dihedral_angle_d12.8722173
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 (%)
2.0023-2.05650.27281280.22082551267997
2.0565-2.1170.26271330.21152600273399
2.117-2.18530.24461440.19582607275199
2.1853-2.26340.23211260.18492632275899
2.2634-2.35410.2491300.17592633276399
2.3541-2.46120.22281380.174226122750100
2.4612-2.59090.23591310.17426462777100
2.5909-2.75330.24381330.173626592792100
2.7533-2.96580.19861470.16382646279399
2.9658-3.26420.22191370.169826662803100
3.2642-3.73640.19311650.157826662831100
3.7364-4.70680.14861420.13327072849100
4.7068-47.64520.16061610.16432822298399
Refinement TLS params.Method: refined / Origin x: -22.1556 Å / Origin y: 3.9029 Å / Origin z: -13.944 Å
111213212223313233
T0.1311 Å20.0177 Å2-0.0006 Å2-0.1516 Å2-0.0291 Å2--0.17 Å2
L0.434 °20.2209 °2-0.0227 °2-0.9542 °2-0.496 °2--1.6499 °2
S0.035 Å °-0.0365 Å °0.0325 Å °0.0721 Å °-0.0075 Å °0.0788 Å °-0.0351 Å °-0.0548 Å °-0.0068 Å °
Refinement TLS groupSelection details: all

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