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- PDB-8swl: Substrate free structure of cytochrome P450 CYP105Q4 from mycobac... -

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Basic information

Entry
Database: PDB / ID: 8swl
TitleSubstrate free structure of cytochrome P450 CYP105Q4 from mycobacterium marinum
ComponentsCytochrome P450 105Q4 Cyp105Q4
KeywordsOXIDOREDUCTASE / CYP105Q4 Cytochrome P450
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, B-class / 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 / TRIETHYLENE GLYCOL / Cytochrome P450 105Q4 Cyp105Q4
Similarity search - Component
Biological speciesMycobacterium marinum ATCC BAA-535 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.06 Å
AuthorsMohamed, H.A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT140100355 Australia
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Structural determination and characterisation of the CYP105Q4 cytochrome P450 enzyme from Mycobacterium marinum.
Authors: Mohamed, H. / Child, S.A. / Doherty, D.Z. / Bruning, J.B. / Bell, S.G.
History
DepositionMay 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 105Q4 Cyp105Q4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0413
Polymers45,2751
Non-polymers7672
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.563, 64.734, 127.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Cytochrome P450 105Q4 Cyp105Q4


Mass: 45274.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum ATCC BAA-535 (bacteria)
Strain: ATCC BAA-535 / M / Gene: cyp105Q4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HG54
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.63 Å3/Da / Density meas: 1 Mg/m3 / Density % sol: 53.21 % / Description: Needle-shaped crystals
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 6.5 / Details: citric acid, bis-trispropane, PEG 3,350 / PH range: 6.5-7.5

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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: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.06→43.02 Å / Num. obs: 9500 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.437 / Net I/σ(I): 6.3 / Num. measured all: 125124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
3.06-3.2712.91.7472154216720.6221.799.6
8.66-43.0211.60.08455894830.99821.799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→43.02 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 466 4.93 %
Rwork0.1988 8986 -
obs0.2031 9452 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.44 Å2 / Biso mean: 50.1457 Å2 / Biso min: 22.91 Å2
Refinement stepCycle: final / Resolution: 3.06→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 53 1 2948
Biso mean--44.31 36.6 -
Num. residues----377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.06-3.50.32651410.257329283069
3.5-4.410.29071740.190929473121
4.41-43.020.26861510.179931113262

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