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- PDB-2w0b: CYP51 OF M. TUBERCULOSIS BOUND TO AN INHIBITOR 3-{[(4-METHYLPHENY... -

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Basic information

Entry
Database: PDB / ID: 2w0b
TitleCYP51 OF M. TUBERCULOSIS BOUND TO AN INHIBITOR 3-{[(4-METHYLPHENYL)SULFONYL]AMINO}PROPYL PYRIDIN-4-YLCARBAMATE
ComponentsCYTOCHROME P450 51
KeywordsOXIDOREDUCTASE / STEROID BIOSYNTHESIS / PROTEIN-INHIBITOR COMPLEX / METAL-BINDING / LIPID SYNTHESIS / NADP / IRON / HEME / CYTOPLASM / MONOOXYGENASE / STEROL BIOSYNTHESIS
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
Chem-CMW / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase / Sterol 14alpha-demethylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPodust, L.M.
CitationJournal: Plos Negl Trop Dis / Year: 2009
Title: Trypanosoma cruzi CYP51 inhibitor derived from a Mycobacterium tuberculosis screen hit.
Authors: Chen, C.K. / Doyle, P.S. / Yermalitskaya, L.V. / Mackey, Z.B. / Ang, K.K. / McKerrow, J.H. / Podust, L.M.
History
DepositionAug 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 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 / 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

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Assembly

Deposited unit
A: CYTOCHROME P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4433
Polymers51,4771
Non-polymers9662
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.710, 84.813, 110.255
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 / / CYP51 / CYPLI / P450-LIA1 / STEROL 14-ALPHA DEMETHYLASE / LANOSTEROL 14-ALPHA DEMETHYLASE / P450-14DM


Mass: 51477.285 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 4XHIS TAG AT THE C-TERMINUS / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0A512, UniProt: P9WPP9*PLUS, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMW / 3-{[(4-methylphenyl)sulfonyl]amino}propyl pyridin-4-ylcarbamate


Mass: 349.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 37 TO LEU ENGINEERED RESIDUE IN CHAIN A, CYS 442 TO ALA
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS A 394 CMW: COORDINATION BOND TO HEME IRON
Sequence detailsMUTATIONS C37L, C442A ENGINEERED 4XHIS TAG AT THE C- TERMINUS

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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: 2.09 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growTemperature: 296 K / pH: 7.5
Details: 15% PEG4000, 2% ISOPROPANOL, 0.1 M HEPES, PH=7.5, T=23 C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 5, 2006
Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING DOUBLE MIRROR
RadiationMonochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 63021 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.1
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8V

1x8v


Resolution: 1.56→67.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.695 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-2, 216-222, 450-451 ARE DISORDERED DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.201 6359 10.1 %RANDOM
Rwork0.164 ---
obs0.168 56603 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.56→67.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 67 380 3946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213703
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9965027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.722.688186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29715607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5071540
X-RAY DIFFRACTIONr_chiral_restr0.0830.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212910
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_it0.9821.52224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63523569
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.81831479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0724.51458
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 462
Rwork0.175 3987

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