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- PDB-6dcd: Mycobacterium marinum cytochrome P450 CYP150A6 in the substrate-f... -

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Basic information

Entry
Database: PDB / ID: 6dcd
TitleMycobacterium marinum cytochrome P450 CYP150A6 in the substrate-free form
ComponentsCytochrome P450 150A6 Cyp150A6
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenase / heme protein
Function / homologyoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / iron ion binding / heme binding / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 150A6 Cyp150A6
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsChild, S.A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT140100355 Australia
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum.
Authors: Child, S.A. / Flint, K.L. / Bruning, J.B. / Bell, S.G.
History
DepositionMay 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 150A6 Cyp150A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3952
Polymers47,7791
Non-polymers6161
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-23 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.570, 80.570, 134.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytochrome P450 150A6 Cyp150A6


Mass: 47778.801 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: cyp150A6, MMAR_4694 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HFD6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.2 M ammonium phosphate, 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9857 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9857 Å / Relative weight: 1
ReflectionResolution: 1.55→48.47 Å / Num. obs: 74838 / % possible obs: 100 % / Redundancy: 22 % / Biso Wilson estimate: 16.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.057 / Rrim(I) all: 0.269 / Net I/σ(I): 11.7 / Num. measured all: 1649781 / Scaling rejects: 241
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.5720.74.7167564536550.2741.0564.8340.8100
8.46-48.4717.30.04693585420.9990.0110.0484499.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48.47 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2458 3655 4.89 %
Rwork0.2219 --
obs0.223 74763 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.98 Å2 / Biso mean: 25.4974 Å2 / Biso min: 8.41 Å2
Refinement stepCycle: final / Resolution: 1.55→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 43 384 3658
Biso mean--24.34 39.27 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043476
X-RAY DIFFRACTIONf_angle_d0.7964760
X-RAY DIFFRACTIONf_chiral_restr0.044510
X-RAY DIFFRACTIONf_plane_restr0.005641
X-RAY DIFFRACTIONf_dihedral_angle_d17.4042121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.545-1.56540.32331380.350627032841
1.5654-1.58680.35131510.336926952846
1.5868-1.60950.3941220.337527132835
1.6095-1.63350.33581610.325926692830
1.6335-1.6590.30591290.313727242853
1.659-1.68620.33331240.307727242848
1.6862-1.71530.30781460.296227032849
1.7153-1.74650.32541290.284427342863
1.7465-1.78010.30561520.279226762828
1.7801-1.81640.2931550.279626802835
1.8164-1.85590.29521610.276926972858
1.8559-1.89910.3031180.266827232841
1.8991-1.94660.2391430.250727002843
1.9466-1.99920.24481510.239727432894
1.9992-2.05810.26461240.238827342858
2.0581-2.12450.27111450.225927242869
2.1245-2.20040.21641230.220227282851
2.2004-2.28850.21251420.220327332875
2.2885-2.39270.25291260.21227462872
2.3927-2.51880.29021220.211627732895
2.5188-2.67660.21941300.215427452875
2.6766-2.88320.25761460.211127682914
2.8832-3.17340.2241320.217627802912
3.1734-3.63240.23371730.196427532926
3.6324-4.57590.20141470.164828092956
4.5759-48.49350.18371650.167729313096
Refinement TLS params.Method: refined / Origin x: 7.1475 Å / Origin y: 37.2014 Å / Origin z: 49.4131 Å
111213212223313233
T0.0578 Å20.0221 Å2-0.0155 Å2-0.1219 Å2-0.0292 Å2--0.093 Å2
L0.2632 °20.068 °2-0.1002 °2--0.0354 °20.3689 °2--0.2129 °2
S0.0019 Å °0.0767 Å °0.0339 Å °0.0673 Å °0.0127 Å °0.0787 Å °-0.1104 Å °-0.1113 Å °-0.0401 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 424
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 393

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