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- PDB-2bz9: Ligand-free structure of sterol 14alpha-demethylase from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 2bz9
TitleLigand-free structure of sterol 14alpha-demethylase from Mycobacterium tuberculosis in P2(1) space group
ComponentsSTEROL 14ALPHA-DEMETHYLASE
KeywordsELECTRON TRANSPORT / STEROL 14ALPHA-DEMETHYLASE / P450 / HEME / IRON / LIPID SYNTHESIS / METAL-BINDING / MONOOXYGENASE
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 / Lanosterol 14-alpha demethylase / Sterol 14alpha-demethylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsYermalitskaya, L.V. / Waterman, M.R. / Podust, L.M.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2007
Title: Small Molecule Scaffolds for Cyp51 Inhibitors Identified by High Throughput Screening and Defined by X-Ray Crystallography
Authors: Podust, L.M. / Von Kries, J.P. / Eddine, A.N. / Kim, Y. / Yermalitskaya, L.V. / Kuehne, R. / Ouellet, H. / Warrier, T. / Altekoster, M. / Lee, J.-S. / Rademann, J. / Oschkinat, H. / ...Authors: Podust, L.M. / Von Kries, J.P. / Eddine, A.N. / Kim, Y. / Yermalitskaya, L.V. / Kuehne, R. / Ouellet, H. / Warrier, T. / Altekoster, M. / Lee, J.-S. / Rademann, J. / Oschkinat, H. / Kaufmann, S.H.E. / Waterman, M.R.
History
DepositionAug 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2006Provider: 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1884
Polymers102,9552
Non-polymers1,2332
Water3,891216
1
A: STEROL 14ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0942
Polymers51,4771
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: STEROL 14ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0942
Polymers51,4771
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.910, 110.340, 99.627
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein STEROL 14ALPHA-DEMETHYLASE


Mass: 51477.285 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / 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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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 ...ENGINEERED RESIDUE IN CHAIN A, CYS 37 TO LEU ENGINEERED RESIDUE IN CHAIN A, CYS 442 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 37 TO LEU ENGINEERED RESIDUE IN CHAIN B, CYS 442 TO ALA CATALYZES C14-DEMETHYLATION OF LANOSTEROL, 24,25-DIHYDROLANOSTEROL AND OBTUSIFOLIOL WHICH IS NECESSARY FOR ERGOSTEROL BIOSYNTHESIS. IT TRANSFORMS LANOSTEROL INTO 4,4'-DIMETHYL CHOLESTA-8,14,24-TRIENE-3-BETA-OL. ITS PRECISE BIOLOGICAL SUBSTRATE IS NOT KNOWN.
Sequence detailsMUTATIONS C37L, C442A, AND 4XHIS TAG AT THE C-TERMINUS ARE ENGINEERED

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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: 2.15 Å3/Da / Density % sol: 42.23 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.5
Details: 25% PEG 4000 4% ISOPROPANOL 0.1 M HEPES, 7.5 T=20 C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9919
DetectorType: MAR300 / Detector: CCD / Date: Nov 9, 2004
Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING MIRROR
RadiationMonochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 45446 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8V

1x8v


Resolution: 2.21→36.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 211089.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3925 10 %RANDOM
Rwork0.215 ---
obs0.215 39163 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7794 Å2 / ksol: 0.406196 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-4.96 Å20 Å2-0.33 Å2
2---6.31 Å20 Å2
3---1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.21→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6816 0 86 216 7118
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 321 10.3 %
Rwork0.261 2794 -
obs--40.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3HEM.PARHEM.TOP

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