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- PDB-1h5z: CYTOCHROME P450 14 ALPHA-STEROL DEMETHYLASE (CYP51) FROM MYCOBACT... -

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Basic information

Entry
Database: PDB / ID: 1h5z
TitleCYTOCHROME P450 14 ALPHA-STEROL DEMETHYLASE (CYP51) FROM MYCOBACTERIUM TUBERCULOSIS IN FERRIC LOW-SPIN STATE
ComponentsCYTOCHROME P450 51
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / 14 ALPHA-STEROL DEMETHYLASE / FERRIC LOW-SPIN / STEROL BIOSYNTHESIS / MONOOXYGENASE / ELECTRON TRANSPORT
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPodust, L.M. / Arase, M. / Waterman, M.R.
Citation
Journal: Structure / Year: 2004
Title: Estriol Bound and Ligand-Free Structures of Sterol 14Alpha-Demethylase.
Authors: Podust, L.M. / Yermalitskaya, L.V. / Lepesheva, G.I. / Podust, V.N. / Dalmasso, E.A. / Waterman, M.R.
#1: Journal: J.Inorg.Biochem. / Year: 2001
Title: Substrate Recognition Sites in 14Alpha-Sterol Demethylase from Comparative Analysis of Amino Acid Sequences and X-Ray Structure of Mycobacterium Tuberculosis Cyp51.
Authors: Podust, L.M. / Stojan, J. / Poulos, T.L. / Waterman, M.R.
#2: Journal: 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
DepositionMay 31, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Aug 5, 2015Group: Derived calculations / Other / Source and taxonomy
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / 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 / struct_site
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.pdbx_dist_value / _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)52,1723
Polymers51,4991
Non-polymers6722
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.489, 84.827, 110.025
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 / STEROL 14-ALPHA DEMETHYLASE / LANOSTEROL 14-ALPHA DEMETHYLASE / P450-14DM


Mass: 51499.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS 394 BINDS HEME IRON / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Cellular location: CYTOPLASM / Gene: CYP51, RV0764C, MTCY369.09C / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174
References: UniProt: P77901, UniProt: P9WPP9*PLUS, sterol 14alpha-demethylase
#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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFOUR HIS RESIDUES WERE ENGINEERED AT 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: 2.132 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 295 K / pH: 6.5 / Details: 20% PEG 4000, 0.1 M NA CACODYLATE, PH 6.5, 22 C
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.2 mMprotein1drop
210 mMTris-HCl1droppH7.5
350 mM1dropNaCl
420 %PEG40001reservoir
510 %isopropanol1reservoir
60.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Mar 22, 2001 / 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: 2.05→40 Å / Num. obs: 25277 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.105 / Net I/σ(I): 10.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.457 / % possible all: 90.9
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 40 Å / % possible obs: 90.6 % / Redundancy: 4.1 % / Num. measured all: 103288 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 90.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E9X

1e9x


Resolution: 2.05→35.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 203124.28 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HIS TAG ON THE C-TERMINAL
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2415 9.9 %RANDOM
Rwork0.185 ---
obs0.185 24451 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.054 Å2 / ksol: 0.375135 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-4.58 Å20 Å20 Å2
2---3.98 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.05→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 44 280 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 347 9.1 %
Rwork0.239 3478 -
obs--83.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEM.PARHEM.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.PARAM
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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