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- PDB-6fmo: Crystal structure of the substrate (obtusifoliol)-bound and ligan... -

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Basic information

Entry
Database: PDB / ID: 6fmo
TitleCrystal structure of the substrate (obtusifoliol)-bound and ligand-free I105F mutant of sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi
ComponentsSterol 14alpha-demethylase
KeywordsPROTEIN BINDING / sterol biosynthesis / CYP51 / OXIDOREDUCTASE / MONOOXYGENASE / SUBSTRATE BINDING
Function / homology
Function and homology information


sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / sterol 14alpha-demethylase / 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
Obtusifoliol / PROTOPORPHYRIN IX CONTAINING FE / Sterol 14alpha-demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
Funding support1items
OrganizationGrant numberCountry
GM 067871
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Binding of a physiological substrate causes large-scale conformational reorganization in cytochrome P450 51.
Authors: Hargrove, T.Y. / Wawrzak, Z. / Fisher, P.M. / Child, S.A. / Nes, W.D. / Guengerich, F.P. / Waterman, M.R. / Lepesheva, G.I.
History
DepositionFeb 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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 / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterol 14alpha-demethylase
B: Sterol 14alpha-demethylase
C: Sterol 14alpha-demethylase
D: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,05111
Polymers221,3054
Non-polymers3,7467
Water905
1
A: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3693
Polymers55,3261
Non-polymers1,0432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3693
Polymers55,3261
Non-polymers1,0432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3693
Polymers55,3261
Non-polymers1,0432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9432
Polymers55,3261
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.310, 154.310, 178.876
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 31 - 478 / Label seq-ID: 31 - 478

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Sterol 14alpha-demethylase


Mass: 55326.188 Da / Num. of mol.: 4 / Mutation: I105F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: CYP51A / Production host: Escherichia coli (E. coli) / Variant (production host): HMS174
References: UniProt: M1FYE4, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DVE / Obtusifoliol


Mass: 426.717 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C30H50O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Obtusifoliol, PEG 4000, potassium phosphate, sodium chloride
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2017 / Details: focusing mirrors
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 3.18→133.64 Å / Num. obs: 38484 / % possible obs: 99.3 % / Redundancy: 6.2 % / CC1/2: 0.386 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.6
Reflection shellResolution: 3.18→3.27 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2990 / Rpim(I) all: 0.697 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ck8

4ck8


Resolution: 3.18→133.64 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU B: 33.432 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29289 2141 5.3 %RANDOM
Rwork0.25988 ---
obs0.26162 38484 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 156.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.35 Å2-0 Å2
2---0.71 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 3.18→133.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14175 0 265 5 14445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01914986
X-RAY DIFFRACTIONr_bond_other_d0.0050.0214186
X-RAY DIFFRACTIONr_angle_refined_deg0.8461.99120345
X-RAY DIFFRACTIONr_angle_other_deg0.6773.00332886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96651788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39323.432676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.248152628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.14715116
X-RAY DIFFRACTIONr_chiral_restr0.050.22199
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02116418
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023094
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_it13.115.6677164
X-RAY DIFFRACTIONr_mcbond_other13.115.6667163
X-RAY DIFFRACTIONr_mcangle_it20.23523.4818948
X-RAY DIFFRACTIONr_mcangle_other20.23523.4828949
X-RAY DIFFRACTIONr_scbond_it11.58616.0257822
X-RAY DIFFRACTIONr_scbond_other11.58316.0267820
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.45123.74811397
X-RAY DIFFRACTIONr_long_range_B_refined26.84917781
X-RAY DIFFRACTIONr_long_range_B_other26.8517780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A295740.06
12B295740.06
21A291040.08
22C291040.08
31A277760.12
32D277760.12
41B294780.06
42C294780.06
51B277220.12
52D277220.12
61C276140.12
62D276140.12
LS refinement shellResolution: 3.184→3.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 147 -
Rwork0.366 2805 -
obs--98.53 %

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