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- PDB-6a15: Structure of CYP90B1 in complex with cholesterol -

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Basic information

Entry
Database: PDB / ID: 6a15
TitleStructure of CYP90B1 in complex with cholesterol
ComponentsCytochrome P450 90B1
KeywordsOXIDOREDUCTASE / cytochrome P450 / phytohormone / brassinosteroid / cholesterol
Function / homology
Function and homology information


steroid 22S-hydroxylase / steroid 22-alpha hydroxylase activity / brassinosteroid biosynthetic process / fatty acid 2-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 2-hydroxylase activity / leaf shaping / response to brassinosteroid / unidimensional cell growth / jasmonic acid mediated signaling pathway / leaf development / response to jasmonic acid / sterol metabolic process / 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
CHOLESTEROL / PROTOPORPHYRIN IX CONTAINING FE / Steroid (22S)-hydroxylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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)54,2719
Polymers52,7721
Non-polymers1,4998
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-23 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.818, 80.574, 83.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 52771.801 Da / Num. of mol.: 1
Mutation: M1-L28 was substituted with MA. E256-V277 and N434-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, 309 molecules

#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-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1 M trisodium citrate (pH4.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→41.52 Å / Num. obs: 49003 / % possible obs: 99.38 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1178 / Rrim(I) all: 0.1335 / Net I/σ(I): 9.61
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4866 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 48938 / CC1/2: 0.796 / Rrim(I) all: 0.5669 / % possible all: 96.52

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: 000)refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A18

6a18


Resolution: 1.79→41.516 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.82
RfactorNum. reflection% reflection
Rfree0.187 2523 5.16 %
Rwork0.1579 --
obs0.1594 48938 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→41.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3559 0 102 301 3962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173748
X-RAY DIFFRACTIONf_angle_d1.3895067
X-RAY DIFFRACTIONf_dihedral_angle_d16.8152210
X-RAY DIFFRACTIONf_chiral_restr0.097541
X-RAY DIFFRACTIONf_plane_restr0.009632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.82450.26551390.21772445X-RAY DIFFRACTION95
1.8245-1.86170.23281410.19312480X-RAY DIFFRACTION98
1.8617-1.90220.24041060.17552573X-RAY DIFFRACTION99
1.9022-1.94640.20871170.16632565X-RAY DIFFRACTION100
1.9464-1.99510.19581450.16482552X-RAY DIFFRACTION100
1.9951-2.0490.20011180.15172592X-RAY DIFFRACTION100
2.049-2.10930.19181310.14832568X-RAY DIFFRACTION100
2.1093-2.17740.17761630.1482553X-RAY DIFFRACTION100
2.1774-2.25520.18121310.15122567X-RAY DIFFRACTION100
2.2552-2.34550.19341350.15342588X-RAY DIFFRACTION100
2.3455-2.45230.18311340.14992579X-RAY DIFFRACTION100
2.4523-2.58150.19161650.15642555X-RAY DIFFRACTION100
2.5815-2.74320.19211500.15512568X-RAY DIFFRACTION100
2.7432-2.9550.2011730.15922574X-RAY DIFFRACTION100
2.955-3.25230.21331300.15972618X-RAY DIFFRACTION100
3.2523-3.72260.16171410.15022623X-RAY DIFFRACTION100
3.7226-4.68910.14461820.13942614X-RAY DIFFRACTION100
4.6891-41.52660.21791220.17882801X-RAY DIFFRACTION99

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