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- PDB-7les: Acanthamoeba castellanii CYP51 (AcCYP51)-Imidazole complex -

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Basic information

Entry
Database: PDB / ID: 7les
TitleAcanthamoeba castellanii CYP51 (AcCYP51)-Imidazole complex
ComponentsObtusifoliol 14alphademethylase, putative
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
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Obtusifoliol 14alphademethylase, putative
Similarity search - Component
Biological speciesAcanthamoeba castellanii str. Neff (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSharma, V. / Podust, L.M.
CitationJournal: Biochemistry / Year: 2022
Title: Homodimerization Counteracts the Detrimental Effect of Nitrogenous Heme Ligands on the Enzymatic Activity of Acanthamoeba castellanii CYP51.
Authors: Nienhaus, K. / Sharma, V. / Nienhaus, G.U. / Podust, L.M.
History
DepositionJan 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Obtusifoliol 14alphademethylase, putative
B: Obtusifoliol 14alphademethylase, putative
C: Obtusifoliol 14alphademethylase, putative
D: Obtusifoliol 14alphademethylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,30621
Polymers209,7894
Non-polymers3,51717
Water66737
1
A: Obtusifoliol 14alphademethylase, putative
B: Obtusifoliol 14alphademethylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,67611
Polymers104,8952
Non-polymers1,7829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-72 kcal/mol
Surface area36950 Å2
MethodPISA
2
C: Obtusifoliol 14alphademethylase, putative
D: Obtusifoliol 14alphademethylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,63010
Polymers104,8952
Non-polymers1,7368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-73 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.560, 125.580, 100.510
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Obtusifoliol 14alphademethylase, putative


Mass: 52447.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 42 N terminal residues were replaced with leading sequence MAKKTSSKGK. 6xHis tag was added to 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, 54 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.65 %
Description: single needle shaped red crystals of 0.5 mm size
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 16%PEG 3350, 2% Tacsimate pH 7.0, 0.1 M sodium citrate pH 5.2

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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: Dec 10, 2020 / 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: 2.65→100.71 Å / Num. obs: 71061 / % possible obs: 99.9 % / Observed criterion σ(I): 0.3 / Redundancy: 6.86 % / Biso Wilson estimate: 78.1 Å2 / Rmerge(I) obs: 0.13 / Net I/av σ(I): 1.44 / Net I/σ(I): 12.45
Reflection shellResolution: 2.65→2.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.98 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 5200 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q2C

6q2c


Resolution: 2.65→100.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.923 / SU B: 19.882 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 0.639 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27535 3178 4.5 %RANDOM
Rwork0.19243 ---
obs0.19611 67857 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.976 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å2-0.87 Å2
2--0.43 Å20 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.65→100.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14261 0 243 37 14541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914916
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214182
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9920226
X-RAY DIFFRACTIONr_angle_other_deg0.986332617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79951799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16923.674675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.279152492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4561593
X-RAY DIFFRACTIONr_chiral_restr0.0880.22163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116791
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023508
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_it4.8477.9387193
X-RAY DIFFRACTIONr_mcbond_other4.8477.9387194
X-RAY DIFFRACTIONr_mcangle_it7.34111.9048993
X-RAY DIFFRACTIONr_mcangle_other7.34111.9058994
X-RAY DIFFRACTIONr_scbond_it4.9058.3197723
X-RAY DIFFRACTIONr_scbond_other4.9058.3197717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.69512.26111234
X-RAY DIFFRACTIONr_long_range_B_refined10.17362.44916411
X-RAY DIFFRACTIONr_long_range_B_other10.17362.45216412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 223 -
Rwork0.396 4971 -
obs--99.87 %

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