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- PDB-7tef: Cytochrome P450 14 alpha-sterol demethylase CYP51 from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 7tef
TitleCytochrome P450 14 alpha-sterol demethylase CYP51 from Mycobacterium marinum
ComponentsCytochrome P450 51B1 Cyp51B1
KeywordsOXIDOREDUCTASE / 14 alpha sterol demethylase Cytochrome P450 Substrate free
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 51B1 Cyp51B1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsMohamed, H.A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT140100355 Australia
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2022
Title: A comparison of the bacterial CYP51 cytochrome P450 enzymes from Mycobacterium marinum and Mycobacterium tuberculosis.
Authors: Mohamed, H. / Child, S.A. / Bruning, J.B. / Bell, S.G.
History
DepositionJan 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: Cytochrome P450 51B1 Cyp51B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7478
Polymers52,4411
Non-polymers1,3067
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.934, 73.112, 89.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 51B1 Cyp51B1


Mass: 52441.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: cyp51B1, MMAR_4932 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HH81
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density meas: 1 Mg/m3 / Density % sol: 45.04 % / Description: Needle-shaped crystals
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 6.5 / Details: Bis-Tris, PEG 3350, ammonium sulfate / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jun 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→44.28 Å / Num. obs: 33253 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.27 / Net I/σ(I): 9.3 / Num. measured all: 447875 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.98-2.0313.31.943074023120.6011.599.5
9.07-44.2812.20.0415004410146.299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA1

1ea1


Resolution: 1.98→44.28 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1709 5.15 %
Rwork0.1723 31484 -
obs0.1744 33193 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.78 Å2 / Biso mean: 26.3023 Å2 / Biso min: 9.24 Å2
Refinement stepCycle: final / Resolution: 1.98→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 25 454 4013
Biso mean--59.6 33.66 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.98-2.040.26471350.231225842719
2.04-2.10.2511440.21125672711
2.1-2.180.27031380.198425892727
2.18-2.270.25221630.189625792742
2.27-2.370.22571450.181525892734
2.37-2.490.24071530.175425822735
2.49-2.650.22471330.178626052738
2.65-2.850.23181410.175326312772
2.85-3.140.23451410.174426082749
3.14-3.60.20031170.157626802797
3.6-4.530.16091740.134926452819
4.53-44.280.20041250.179828252950

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