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- PDB-6ux0: Isavuconazole bound complex of Acanthamoeba castellanii CYP51 -

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Basic information

Entry
Database: PDB / ID: 6ux0
TitleIsavuconazole bound complex of Acanthamoeba castellanii CYP51
ComponentsObtusifoliol 14alphademethylase
KeywordsOXIDOREDUCTASE / cyp51 / ergosterol biosynthesis / Acanthamoeba / 14- alpha-demethylase / Isavuconazole
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Chem-QKM / Obtusifoliol 14alphademethylase, putative
Similarity search - Component
Biological speciesAcanthamoeba castellanii str. Neff (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 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
DepositionNov 6, 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 1.2Jul 6, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Obtusifoliol 14alphademethylase
B: Obtusifoliol 14alphademethylase
C: Obtusifoliol 14alphademethylase
D: Obtusifoliol 14alphademethylase
E: Obtusifoliol 14alphademethylase
F: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,11920
Polymers314,6846
Non-polymers6,43514
Water181
1
A: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5013
Polymers52,4471
Non-polymers1,0542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5574
Polymers52,4471
Non-polymers1,1103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5013
Polymers52,4471
Non-polymers1,0542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5013
Polymers52,4471
Non-polymers1,0542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5013
Polymers52,4471
Non-polymers1,0542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5574
Polymers52,4471
Non-polymers1,1103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.450, 99.060, 108.710
Angle α, β, γ (deg.)92.610, 96.200, 120.090
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Obtusifoliol 14alphademethylase


Mass: 52447.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-QKM / 4-{2-[(2R,3R)-3-(2,5-difluorophenyl)-3-hydroxy-4-(1H-1,2,4-triazol-1-yl)butan-2-yl]-1,3-thiazol-4-yl}benzonitrile / Isavuconazole


Mass: 437.465 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H17F2N5OS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antifungal*YM
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.92 Å3/Da / Density % sol: 57.84 %
Description: single pyramid shaped red crystals of 0.05-0.1 mm size.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1 M tri-sodium citrate, pH 5.6; 12% w/v PEG 3350

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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: Oct 22, 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: 2.93→107.35 Å / Num. obs: 74605 / % possible obs: 97.9 % / Redundancy: 3.397 % / Biso Wilson estimate: 83.087 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.193 / Rrim(I) all: 0.229 / Χ2: 0.942 / Net I/σ(I): 5.33 / Num. measured all: 253407 / Scaling rejects: 118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.93-3.013.4493.4270.319161567355560.134.06197.9
3.01-3.093.4222.4420.4318408548053800.1952.89698.2
3.09-3.183.2171.9040.5416653529751760.2592.29497.7
3.18-3.283.311.4270.7516771517350670.411.70898
3.28-3.383.5651.0261.1217659506049540.6071.20897.9
3.38-3.53.5110.8621.3716882489848090.671.01798.2
3.5-3.633.4880.6341.8815864464845480.8180.74997.8
3.63-3.783.4180.4452.7115065452144070.8770.52997.5
3.78-3.953.3340.3093.6814041435242120.9370.36996.8
3.95-4.143.1210.2314.7612470413839960.9460.28196.6
4.14-4.373.2820.1886.0912677394038620.9660.22598
4.37-4.633.5660.1388.5313014370936490.9860.16298.4
4.63-4.953.5260.1179.712352354935030.9870.13898.7
4.95-5.353.4870.129.5711084322431790.9850.14298.6
5.35-5.863.3570.1268.969977301029720.9820.1598.7
5.86-6.553.1380.10310.388391269126740.9840.12599.4
6.55-7.573.5750.06815.048398239423490.9960.0898.1
7.57-9.273.4430.04222.646742200619580.9970.0597.6
9.27-13.13.1420.031274772156515190.9980.03897.1
13.1-107.353.6240.03131.1730268568350.9980.03697.5

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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: 2.93→107.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.877 / SU B: 36.102 / SU ML: 0.595 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3081 3621 5.1 %RANDOM
Rwork0.2128 ---
obs0.2176 67944 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.62 Å2 / Biso mean: 98.861 Å2 / Biso min: 37.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20.81 Å20.36 Å2
2---2.84 Å2-0.57 Å2
3---3.98 Å2
Refinement stepCycle: final / Resolution: 2.93→107.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19552 0 446 1 19999
Biso mean--72.3 41.37 -
Num. residues----2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01920536
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219059
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.99527953
X-RAY DIFFRACTIONr_angle_other_deg1.0653.00343644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.33452475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79123.712951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.474153252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.13415134
X-RAY DIFFRACTIONr_chiral_restr0.090.22996
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02123369
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024911
LS refinement shellResolution: 2.93→3.006 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 164 -
Rwork0.422 3341 -
all-3505 -
obs--61.83 %

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