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- PDB-7uwp: Detergent-bound CYP51 from Acanthamoeba castellanii -

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Basic information

Entry
Database: PDB / ID: 7uwp
TitleDetergent-bound CYP51 from Acanthamoeba castellanii
Componentssterol 14a-demethylase
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / CYP51 / STEROL 14 ALPHA- DEMETHYLASE / sterol biosynthesis
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 / Obtusifoliol 14alphademethylase, putative
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM067871 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Identification of Potent and Selective Inhibitors of Acanthamoeba: Structural Insights into Sterol 14-Demethylase as a Key Drug Target
Authors: Hargrove, T.Y. / Lamb, D.C. / Wawrzak, Z. / Hull, M. / Kelly, S.L. / Guengerich, F.P. / Lepesheva, G.I.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sterol 14a-demethylase
B: sterol 14a-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1496
Polymers104,8952
Non-polymers2,2544
Water14,124784
1
A: sterol 14a-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5743
Polymers52,4471
Non-polymers1,1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sterol 14a-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5743
Polymers52,4471
Non-polymers1,1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.397, 101.561, 122.004
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 sterol 14a-demethylase / Obtusifoliol 14alphademethylase / putative


Mass: 52447.324 Da / Num. of mol.: 2 / Mutation: HIS TAG ADDED TO THE C-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS-174 / References: UniProt: L8GJB3, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 3350, potassium phosphate, (2R,3R,4S,5S,6R)-2-(((2R,3S,4R,5R,6R)-6-(dodecyloxy)-4,5-dihydroxy-2-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)oxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 21, 2022 / Details: BE LENS
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 91205 / % possible obs: 89.48 % / Redundancy: 9.5 % / Biso Wilson estimate: 20.5 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rpim(I) all: 0.022 / Rrim(I) all: 0.069 / Net I/σ(I): 34.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1947 / CC1/2: 0.632 / CC star: 0.88 / Rpim(I) all: 0.533 / % possible all: 28

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mcw

6mcw


Resolution: 1.95→28.08 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.806 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 4062 5 %RANDOM
Rwork0.1933 ---
obs0.1949 77442 89.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.39 Å2 / Biso mean: 25.24 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.95→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7122 0 156 784 8062
Biso mean--15.36 33.89 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137470
X-RAY DIFFRACTIONr_bond_other_d0.0020.0157128
X-RAY DIFFRACTIONr_angle_refined_deg1.221.68110130
X-RAY DIFFRACTIONr_angle_other_deg1.2871.61116442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4285886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77122.051390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.953151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4851548
X-RAY DIFFRACTIONr_chiral_restr0.0630.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028312
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021744
LS refinement shellResolution: 1.952→2.003 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 103 -
Rwork0.259 1947 -
all-2050 -
obs--30.75 %

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