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- PDB-6q2c: Domain-swapped dimer of Acanthamoeba castellanii CYP51 -

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Basic information

Entry
Database: PDB / ID: 6q2c
TitleDomain-swapped dimer of Acanthamoeba castellanii CYP51
ComponentsObtusifoliol 14alphademethylase
KeywordsOXIDOREDUCTASE / cyp51 / ergosterol biosynthesis / Acanthamoeba / 14-alpha-demethylase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity / monooxygenase activity / methylation / iron ion binding / heme binding / membrane
Similarity search - Function
: / Cytochrome P450, E-class, group IV / 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 / : / DI(HYDROXYETHYL)ETHER / Obtusifoliol 14alphademethylase, putative
Similarity search - Component
Biological speciesAcanthamoeba castellanii str. Neff (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSharma, V. / Podust, L.M.
CitationJournal: Mol.Pharmacol. / Year: 2020
Title: Domain-Swap Dimerization of Acanthamoeba castellanii CYP51 and a Unique Mechanism of Inactivation by Isavuconazole.
Authors: Sharma, V. / Shing, B. / Hernandez-Alvarez, L. / Debnath, A. / Podust, L.M.
History
DepositionAug 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Obtusifoliol 14alphademethylase
B: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,56010
Polymers104,8952
Non-polymers1,6658
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, gel filtration coupled with multi-angle light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-89 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.350, 101.570, 123.740
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, 2 molecules AB

#1: Protein Obtusifoliol 14alphademethylase


Mass: 52447.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 42 N-terminal residues were replaced with the leading sequence MAKKTSSKGK. 6xHis tag was added at the C-terminus.
Source: (gene. exp.) Acanthamoeba castellanii str. Neff (eukaryote)
Gene: ACA1_372720 / Plasmid: pCW-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 / References: UniProt: L8GJB3

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Non-polymers , 5 types, 518 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#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.: 510 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60.11 % / Description: Red needle shaped crystals of 0.5 mm size.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350; 0.2 M di-sodium DL-malate, pH 6.8-7.2
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: Liquid Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2019 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 115283 / % possible obs: 98.2 % / Observed criterion σ(I): 0.3 / Redundancy: 11.4 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.68
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.86 / Mean I/σ(I) obs: 0.45 / Num. unique obs: 38943 / Χ2: 13.9 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C27

4c27


Resolution: 1.8→78.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.802 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 5783 5 %RANDOM
Rwork0.1853 ---
obs0.1874 109450 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--2.42 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→78.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 110 510 7753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197587
X-RAY DIFFRACTIONr_bond_other_d0.0020.027162
X-RAY DIFFRACTIONr_angle_refined_deg1.9742.00410333
X-RAY DIFFRACTIONr_angle_other_deg1.086316462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93723.687339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.948151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0151547
X-RAY DIFFRACTIONr_chiral_restr0.1370.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218595
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021796
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.324.6983625
X-RAY DIFFRACTIONr_mcbond_other4.3184.6963624
X-RAY DIFFRACTIONr_mcangle_it5.3487.0184540
X-RAY DIFFRACTIONr_mcangle_other5.3477.0214541
X-RAY DIFFRACTIONr_scbond_it5.0955.1353962
X-RAY DIFFRACTIONr_scbond_other5.0945.1353962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1787.4765794
X-RAY DIFFRACTIONr_long_range_B_refined8.70738.2578944
X-RAY DIFFRACTIONr_long_range_B_other8.70738.268945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 377 -
Rwork0.459 6771 -
obs--83.27 %

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