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- PDB-6a17: Crystal structure of CYP90B1 in complex with brassinazole -

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Basic information

Entry
Database: PDB / ID: 6a17
TitleCrystal structure of CYP90B1 in complex with brassinazole
ComponentsCytochrome P450 90B1
KeywordsOXIDOREDUCTASE / cytochrome P450 / phytohormone / brassinosteroid / brassinazole
Function / homology
Function and homology information


steroid 22S-hydroxylase / steroid 22-alpha hydroxylase activity / brassinosteroid biosynthetic process / fatty acid alpha-hydroxylase activity / leaf shaping / response to brassinosteroid / unidimensional cell growth / jasmonic acid mediated signaling pathway / leaf development / response to jasmonic acid ...steroid 22S-hydroxylase / steroid 22-alpha hydroxylase activity / brassinosteroid biosynthetic process / fatty acid alpha-hydroxylase activity / leaf shaping / response to brassinosteroid / unidimensional cell growth / jasmonic acid mediated signaling pathway / leaf development / response to jasmonic acid / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding / heme binding / endoplasmic reticulum / membrane
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
Chem-9RL / PROTOPORPHYRIN IX CONTAINING FE / Steroid (22S)-hydroxylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsFujiyama, K. / Hino, T. / Kanadani, M. / Mizutani, M. / Nagano, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17H05444 Japan
CitationJournal: Nat.Plants / Year: 2019
Title: Structural insights into a key step of brassinosteroid biosynthesis and its inhibition.
Authors: Fujiyama, K. / Hino, T. / Kanadani, M. / Watanabe, B. / Jae Lee, H. / Mizutani, M. / Nagano, S.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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: Cytochrome P450 90B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0857
Polymers52,8861
Non-polymers1,1996
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-24 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.857, 58.857, 539.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 90B1 / Protein DWARF 4 / Dwarf4 / Steroid 22-alpha-hydroxylase


Mass: 52885.902 Da / Num. of mol.: 1
Mutation: M1-L28 was substituted with MA. E256-V277 and N435-S446 were deleted, P506L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP90B1, DWF4, At3g50660, T3A5.40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O64989, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-9RL / (2R,3S)-4-(4-chlorophenyl)-2-phenyl-3-(1H-1,2,4-triazol-1-yl)butan-2-ol


Mass: 327.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.90 M sodium chloride, 0.10 M sodium/potassium phosphate buffer (pH6.2), 10%(w/v) PEG8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.301→49.04 Å / Num. obs: 25669 / % possible obs: 97.24 % / Redundancy: 8.5 % / Biso Wilson estimate: 35.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0789 / Rrim(I) all: 0.08368 / Net I/σ(I): 19.21
Reflection shellResolution: 2.301→2.384 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3575 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1841 / CC1/2: 0.918 / Rrim(I) all: 0.4563 / % possible all: 72.28

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Processing

Software
NameVersionClassification
XDS(1.11.1_2575: ???)data reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX(1.11.1_2575: 000)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A15

6a15


Resolution: 2.301→49.038 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2747 1257 4.9 %
Rwork0.2337 --
obs0.2357 25661 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.301→49.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 80 106 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023781
X-RAY DIFFRACTIONf_angle_d0.5215119
X-RAY DIFFRACTIONf_dihedral_angle_d14.7882227
X-RAY DIFFRACTIONf_chiral_restr0.035539
X-RAY DIFFRACTIONf_plane_restr0.002647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3013-2.39340.3817980.32492008X-RAY DIFFRACTION75
2.3934-2.50240.33761320.29622697X-RAY DIFFRACTION100
2.5024-2.63430.33381340.27122699X-RAY DIFFRACTION100
2.6343-2.79930.34641370.26832746X-RAY DIFFRACTION100
2.7993-3.01540.29531590.26332709X-RAY DIFFRACTION100
3.0154-3.31880.29451490.24212760X-RAY DIFFRACTION100
3.3188-3.79890.24861530.21312785X-RAY DIFFRACTION100
3.7989-4.78560.22841460.19632851X-RAY DIFFRACTION100
4.7856-49.0490.25581490.22073149X-RAY DIFFRACTION100

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