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- PDB-3p99: Sterol 14alpha-demethylase (CYP51) from Trypanosoma brucei in com... -

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Basic information

Entry
Database: PDB / ID: 3p99
TitleSterol 14alpha-demethylase (CYP51) from Trypanosoma brucei in complex with delta7-14alpha-methylene-cyclopropyl-dihydrolanosterol
ComponentsSterol 14-alpha-demethylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 fold/sterol 14-alpha demethylase / CYP51 / monooxygenase / hemoprotein / sterol biosynthesis / cytochrome P450 reductase (CPR) / endoplasmic reticulum / membrane
Function / homology
Function and homology information


membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol metabolic process / bile acid biosynthetic process / cholesterol homeostasis / nuclear envelope / oxidoreductase activity ...membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol metabolic process / bile acid biosynthetic process / cholesterol homeostasis / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum
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 / Chem-LNP / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLepesheva, G.I. / Hargrove, T.Y. / Waterman, M.R. / Wawrzak, Z.
CitationJournal: J.Lipid Res. / Year: 2012
Title: Structural complex of sterol 14alpha-demethylase (CYP51) with 14alpha-methylenecyclopropyl-delta7-24, 25-dihydrolanosterol
Authors: Hargrove, T.Y. / Wawrzak, Z. / Liu, J. / Waterman, M.R. / Nes, W.D. / Lepesheva, G.I.
History
DepositionOct 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)209,02712
Polymers204,6944
Non-polymers4,3338
Water90150
1
A: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.610, 80.570, 115.800
Angle α, β, γ (deg.)107.93, 102.43, 99.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sterol 14-alpha-demethylase


Mass: 51173.395 Da / Num. of mol.: 4 / Fragment: unp residues 29-481 / Mutation: G29P, K30T, L31D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: CYP51, Tb11.02.4080 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q385E8, 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-LNP / (3alpha,9beta,10alpha,13alpha)-30-cyclopropylidenelanost-7-en-3-ol


Mass: 466.781 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H54O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 297 K / pH: 7.2
Details: PEG 3350, POTASSIUM PHOSPHATE; n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE, delta7-14alpha-methylene-cyclopropyl-dihydrolanosterol, pH 7.2, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 / Details: BE LENSES/DIAMOND LAUE MONO
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→29.39 Å / Num. obs: 37941 / % possible obs: 97.6 % / Observed criterion σ(I): 2.6 / Redundancy: 3.8 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.068 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.55 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G1Q

3g1q


Resolution: 3→29.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 51.98 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27144 1894 5 %RANDOM
Rwork0.22313 ---
obs0.2256 36047 97.78 %-
all-36857 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.529 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.35 Å20.57 Å2
2--1.4 Å21.91 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 3→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14197 0 308 50 14555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02214876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8942.02220220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.03151783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06123.231650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.252152589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.19415120
X-RAY DIFFRACTIONr_chiral_restr0.0490.22216
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02111164
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7541.58959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.413214533
X-RAY DIFFRACTIONr_scbond_it2.48935917
X-RAY DIFFRACTIONr_scangle_it4.0124.55675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 145 -
Rwork0.248 2633 -
obs--97.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42890.23230.16582.79380.87952.93770.11870.0339-0.0471-0.2087-0.0925-0.2296-0.2093-0.0971-0.02610.20280.0940.07020.2880.11470.257618.229625.0856-36.6539
21.97120.66950.66473.53581.86215.10050.1846-0.0739-0.0440.37380.2771-0.3563-0.25960.2332-0.46180.28390.06030.07940.19810.01710.359714.4053-35.216914.4858
33.3107-0.08950.06382.4319-0.01062.1435-0.0845-0.04410.06440.27560.00770.1073-0.1270.1840.07680.2475-0.04060.04610.11080.01680.063313.31955.569620.9986
43.9954-0.54360.40495.9863-0.78982.6196-0.0709-0.00740.26790.106-0.0902-0.5018-0.25240.28950.1610.0418-0.0313-0.06780.20060.03430.194132.215-13.5139-31.4347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 476
2X-RAY DIFFRACTION1A482 - 490
3X-RAY DIFFRACTION1A3 - 28
4X-RAY DIFFRACTION1A483 - 491
5X-RAY DIFFRACTION2B29 - 476
6X-RAY DIFFRACTION2B482 - 490
7X-RAY DIFFRACTION2B2 - 22
8X-RAY DIFFRACTION2B483 - 487
9X-RAY DIFFRACTION3C29 - 476
10X-RAY DIFFRACTION3C482 - 490
11X-RAY DIFFRACTION3C13 - 27
12X-RAY DIFFRACTION3C483 - 487
13X-RAY DIFFRACTION4D29 - 476
14X-RAY DIFFRACTION4D482 - 490
15X-RAY DIFFRACTION4D1 - 26
16X-RAY DIFFRACTION4D483 - 486

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