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- PDB-5mog: Oryza sativa phytoene desaturase inhibited by norflurazon -

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Basic information

Entry
Database: PDB / ID: 5mog
TitleOryza sativa phytoene desaturase inhibited by norflurazon
ComponentsPhytoene dehydrogenase, chloroplastic/chromoplastic
KeywordsOXIDOREDUCTASE / Inhibitor / Isomerase / Carotenoid biosynthesis
Function / homology
Function and homology information


15-cis-phytoene desaturase / phytoene dehydrogenase activity / plastid membrane / carotene biosynthetic process / chromoplast / carotenoid biosynthetic process / FAD binding / chloroplast / protein homotetramerization
Similarity search - Function
Phytoene desaturase / : / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / Norflurazon / 15-cis-phytoene desaturase, chloroplastic/chromoplastic
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.77 Å
AuthorsBrausemann, A. / Gemmecker, S. / Koschmieder, J. / Beyer, P. / Einsle, O.
CitationJournal: Structure / Year: 2017
Title: Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation.
Authors: Brausemann, A. / Gemmecker, S. / Koschmieder, J. / Ghisla, S. / Beyer, P. / Einsle, O.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phytoene dehydrogenase, chloroplastic/chromoplastic
B: Phytoene dehydrogenase, chloroplastic/chromoplastic
C: Phytoene dehydrogenase, chloroplastic/chromoplastic
D: Phytoene dehydrogenase, chloroplastic/chromoplastic
E: Phytoene dehydrogenase, chloroplastic/chromoplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,56828
Polymers280,2715
Non-polymers7,29623
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)230.210, 230.210, 179.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Phytoene dehydrogenase, chloroplastic/chromoplastic / Phytoene desaturase


Mass: 56054.254 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: PDS1, PDS, OsI_010044 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3)
References: UniProt: A2XDA1, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors

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Non-polymers , 6 types, 441 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NRF / Norflurazon


Mass: 303.668 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H9ClF3N3O
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 4.46 Å3/Da / Density % sol: 72.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 24 % (w/v) PEG5000 MME, 0.1 M HEPES/NaOH pH 7.0, 2 % (v/v) Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.77→60.25 Å / Num. obs: 118342 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 87.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.165 / Net I/σ(I): 14.2
Reflection shellResolution: 2.77→2.82 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.533 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→60.25 Å / Cor.coef. Fo:Fc: 0.9358 / Cor.coef. Fo:Fc free: 0.9254 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.376 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.252
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 5852 4.95 %RANDOM
Rwork0.2087 ---
obs0.2095 118340 99.97 %-
Displacement parametersBiso max: 238.04 Å2 / Biso mean: 79.54 Å2 / Biso min: 30.99 Å2
Baniso -1Baniso -2Baniso -3
1--3.636 Å20 Å20 Å2
2---3.636 Å20 Å2
3---7.2721 Å2
Refine analyzeLuzzati coordinate error obs: 0.423 Å
Refinement stepCycle: final / Resolution: 2.77→60.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18600 0 486 418 19504
Biso mean--76.36 59.5 -
Num. residues----2345
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8997SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes465HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3053HARMONIC5
X-RAY DIFFRACTIONt_it19585HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2451SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19585HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg26589HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion3.22
LS refinement shellResolution: 2.77→2.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3066 460 5.26 %
Rwork0.2701 8286 -
all0.272 8746 -
obs--99.97 %

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