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- PDB-1e9x: Cytochrome P450 14 alpha-sterol demethylase (CYP51) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 1e9x
TitleCytochrome P450 14 alpha-sterol demethylase (CYP51) from Mycobacterium tuberculosis in complex with 4-phenylimidazole
ComponentsCYTOCHROME P450 51-LIKE RV0764C
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / 14 ALPHA-STEROL DEMETHYLASE / AZOLE INHIBITORS
Function / homology
Function and homology information


sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding ...sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytosol / cytoplasm
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 / 4-PHENYL-1H-IMIDAZOLE / Lanosterol 14-alpha demethylase / Sterol 14alpha-demethylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.1 Å
AuthorsPodust, L.M. / Poulos, T.L. / Waterman, M.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal Structure of Cytochrome P450 14Alpha -Sterol Demethylase (Cyp51) from Mycobacterium Tuberculosis in Complex with Azole Inhibitors
Authors: Podust, L.M. / Poulos, T.L. / Waterman, M.R.
History
DepositionOct 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CYTOCHROME P450 51-LIKE RV0764C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2603
Polymers51,4991
Non-polymers7612
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.136, 83.863, 109.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450 51-LIKE RV0764C / CYP51 / 14ALPHA-STEROL DEMETHYLASE


Mass: 51499.332 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CYS 394 BINDS HEME IRON. 4-PHENYLIMIDAZOLE IS BOUND IN THE ACTIVE SITE COORDINATING HEME IRON AS A SIXTH LIGAND
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Cellular location: CYTOPLASM / Gene: CYP51 OR RV0764C OR MTCY369.09C / Plasmid: PET17B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / References: UniProt: P77901, UniProt: P9WPP9*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PIM / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHIS TAG ON THE C-TERMINAL

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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: 2.04 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5
Details: 20% PEG 400, 10% ISOPROPANOL 0.1 M HEPES, PH=7.5, 4-PHENYLIMIDAZOLE IN SATURATING CONCENTRATION, pH 7.50
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein1drop
220 mMTris-HCl1drop
3250 mM1dropNaCl
40.5 mMEDTA1drop
520 %PEG40001reservoir
610 %isopropanol1reservoir
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 15, 2000 / Details: MIRROR
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 25107 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.111 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.489 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 173919 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 91.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→39.16 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 220663.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2445 9.9 %RANDOM
Rwork0.185 ---
obs0.185 24660 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.5549 Å2 / ksol: 0.371488 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20 Å2
2---2.85 Å20 Å2
3----0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 54 282 3874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 366 9.9 %
Rwork0.231 3333 -
obs--88.7 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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