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- PDB-3g1q: Crystal structure of sterol 14-alpha demethylase (CYP51) from Try... -

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Basic information

Entry
Database: PDB / ID: 3g1q
TitleCrystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in ligand free state
ComponentsSterol 14-alpha-demethylase
KeywordsOXIDOREDUCTASE / sterol 14-alpha demethylase / CYP51 / cytochrome P450 / heme / monooxygenase / membrane protein / sterol biosynthesis
Function / homology
Function and homology information


membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / 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 / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination of molecular replacement, Fe-SAD / Resolution: 1.89 Å
AuthorsLepesheva, G.I. / Hargrove, T.Y. / Harp, J. / Wawrzak, Z. / Waterman, M.R. / Park, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections.
Authors: Lepesheva, G.I. / Park, H.W. / Hargrove, T.Y. / Vanhollebeke, B. / Wawrzak, Z. / Harp, J.M. / Sundaramoorthy, M. / Nes, W.D. / Pays, E. / Chaudhuri, M. / Villalta, F. / Waterman, M.R.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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

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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)206,3718
Polymers203,9054
Non-polymers2,4664
Water8,899494
1
A: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5932
Polymers50,9761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5932
Polymers50,9761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5932
Polymers50,9761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5932
Polymers50,9761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.823, 79.874, 117.146
Angle α, β, γ (deg.)74.21, 81.56, 68.49
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THIS IS A MEMBRANE BOUND PROTEIN THAT IS FUNCTIONALLY A MONOMER AND FORMS COMPLEX WITH THE ELECTRON DONOR PARTNER CYTOCHROME P450 REDUCTASE.

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Components

#1: Protein
Sterol 14-alpha-demethylase / CYP51


Mass: 50976.152 Da / Num. of mol.: 4 / Mutation: T27S, R28K, P29G, T30K, D31L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Cellular location: membrane / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 3350, POTASSIUM PHOSPHATE, n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
SYNCHROTRONAPS 21-ID-D21.73892
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDNov 1, 2008Be Lenses/Diamond Laue Mono
MARMOSAIC 300 mm CCD2CCDNov 1, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2KohzuSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.738921
ReflectionResolution: 1.89→30 Å / Num. all: 153658 / Num. obs: 150278 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 1.89→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.472 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.4.0061refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: combination of molecular replacement, Fe-SAD
Starting model: PDB ENTRY 2VE4

2ve4


Resolution: 1.89→28.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.719 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23423 7519 5 %RANDOM
Rwork0.19522 ---
obs0.19716 142726 97.45 %-
all-146460 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.2 Å20.14 Å2
2--0.02 Å2-0.01 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.89→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14192 0 172 494 14858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02214718
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8942.0119961
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34651781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71923.22649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.951152591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.03415120
X-RAY DIFFRACTIONr_chiral_restr0.1490.22175
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111116
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_it1.321.58953
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.196214522
X-RAY DIFFRACTIONr_scbond_it3.58335765
X-RAY DIFFRACTIONr_scangle_it5.5534.55439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 477 -
Rwork0.264 9925 -
obs--91.68 %

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