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- PDB-6uw2: Clotrimazole bound complex of Acanthamoeba castellanii CYP51 -

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Basic information

Entry
Database: PDB / ID: 6uw2
TitleClotrimazole bound complex of Acanthamoeba castellanii CYP51
ComponentsObtusifoliol 14alphademethylase
KeywordsOXIDOREDUCTASE / cyp51 / ergosterol biosynthesis / Acanthamoeba / 14- alpha-demethylase / Clotrimazole
Function / homology
Function and homology information


steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / methyltransferase activity / cholesterol homeostasis / 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
1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / GUANIDINE / PROTOPORPHYRIN IX CONTAINING FE / Obtusifoliol 14alphademethylase, putative
Similarity search - Component
Biological speciesAcanthamoeba castellanii str. Neff (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 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 4, 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
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)320,62921
Polymers314,6846
Non-polymers5,94515
Water82946
1
A: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4093
Polymers52,4471
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4684
Polymers52,4471
Non-polymers1,0203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4684
Polymers52,4471
Non-polymers1,0203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4093
Polymers52,4471
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4093
Polymers52,4471
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Obtusifoliol 14alphademethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4684
Polymers52,4471
Non-polymers1,0203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.980, 177.220, 181.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-CL6 / 1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / CLOTRIMAZOLE


Mass: 344.837 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H17ClN2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antifungal*YM
#4: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH5N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.02 Å3/Da / Density % sol: 59.34 %
Description: single pyramid shaped red crystals of 0.05-0.1 mm size.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium-cocydylate; 0.12 M Guanidine hydrochloride; 2% Jefframine M-600, pH 7.0

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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: Aug 15, 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: 2.92→127.13 Å / Num. obs: 83269 / % possible obs: 100 % / Redundancy: 13.53 % / Biso Wilson estimate: 70.545 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.401 / Rrim(I) all: 0.417 / Χ2: 0.849 / Net I/σ(I): 7.12 / Num. measured all: 1126634 / Scaling rejects: 190
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
2.92-313.6074.6940.6482306605360490.2644.87699.9
3-3.0814.0933.5780.8983995596059600.383.71100
3.08-3.1714.0212.5811.2680745576057590.5452.677100
3.17-3.2613.842.0931.5977711561756150.6232.172100
3.26-3.3713.6071.7561.974350546554640.7121.824100
3.37-3.4913.0421.4372.3168770527552730.7571.496100
3.49-3.6212.6931.0963.0764364507250710.8511.142100
3.62-3.7713.7210.8444.2967080489148890.9240.877100
3.77-3.9413.8210.5935.9665637475247490.9640.61599.9
3.94-4.1313.8270.4127.8761929447944790.9810.427100
4.13-4.3513.7080.3279.358864429442940.9880.34100
4.35-4.6212.8720.24811.0252595408640860.9890.259100
4.62-4.9413.3290.2112.4751143383738370.9930.218100
4.94-5.3314.150.2212.5450813359135910.9920.228100
5.33-5.8413.8480.24311.3545754330433040.9910.252100
5.84-6.5313.270.21512.0440023301630160.9910.223100
6.53-7.5412.5830.13616.5633583266926690.9950.142100
7.54-9.2313.7370.07925.8831471229122910.9990.082100
9.23-13.0612.4990.0631.2722548180418040.9990.063100
13.06-127.1312.1170.06531.3612953107310690.9990.06899.6

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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: 2.92→127.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.875 / SU B: 27.55 / SU ML: 0.457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.451
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2905 4043 4.9 %RANDOM
Rwork0.209 ---
obs0.2129 79148 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.07 Å2 / Biso mean: 79.017 Å2 / Biso min: 20.84 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å2-0 Å20 Å2
2---3.32 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 2.92→127.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21135 0 420 46 21601
Biso mean--63.85 45.59 -
Num. residues----2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922138
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220822
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.99530098
X-RAY DIFFRACTIONr_angle_other_deg1.02347770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10252679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22923.645985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56153583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.09515137
X-RAY DIFFRACTIONr_chiral_restr0.0880.23230
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125055
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025277
LS refinement shellResolution: 2.92→2.996 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 282 -
Rwork0.389 5762 -
all-6044 -
obs--99.93 %

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