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- PDB-6bld: Mycobacterium marinum cytochrome P450 CYP268A2 in complex with ps... -

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Basic information

Entry
Database: PDB / ID: 6bld
TitleMycobacterium marinum cytochrome P450 CYP268A2 in complex with pseudoionone
ComponentsCytochrome P450 268A2 Cyp268A2
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenase / heme protein
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3E,5E)-6,10-dimethylundeca-3,5,9-trien-2-one / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 268A2 Cyp268A2
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.997 Å
AuthorsChild, S.A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT140100355 Australia
CitationJournal: Biochem. J. / Year: 2018
Title: Structural and functional characterisation of the cytochrome P450 enzyme CYP268A2 from
Authors: Child, S.A. / Naumann, E.F. / Bruning, J.B. / Bell, S.G.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 268A2 Cyp268A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8663
Polymers46,0571
Non-polymers8092
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-23 kcal/mol
Surface area16570 Å2
Unit cell
Length a, b, c (Å)154.759, 44.726, 57.727
Angle α, β, γ (deg.)90.000, 100.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-733-

HOH

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Components

#1: Protein Cytochrome P450 268A2 Cyp268A2


Mass: 46056.918 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: cyp268A2, MMAR_3761 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B2HMF7
#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
#3: Chemical ChemComp-DXJ / (3E,5E)-6,10-dimethylundeca-3,5,9-trien-2-one / Pseudoionone


Mass: 192.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.96 M ammonium phosphate, 0.3 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→42.91 Å / Num. obs: 51043 / % possible obs: 99.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 22.28 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.051 / Rrim(I) all: 0.14 / Net I/σ(I): 9.7 / Num. measured all: 195943 / Scaling rejects: 0
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
2-2.0570.7421212517430.7680.30.802289.4
8.93-42.916.30.04919923180.9980.020.05330.599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata collection
Aimless0.5.25data scaling
CNSphasing
REFMAC5phasing
Cootmodel building
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WM4

2wm4


Resolution: 1.997→37.999 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1846 3.62 %Random Selection
Rwork0.1996 49197 --
obs0.2013 51043 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.17 Å2 / Biso mean: 26.8952 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 1.997→37.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 57 382 3649
Biso mean--15.9 34.4 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023349
X-RAY DIFFRACTIONf_angle_d0.5494567
X-RAY DIFFRACTIONf_chiral_restr0.038492
X-RAY DIFFRACTIONf_plane_restr0.003607
X-RAY DIFFRACTIONf_dihedral_angle_d8.9831978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9974-2.05140.27281160.27723415353188
2.0514-2.11170.31731310.267738143945100
2.1117-2.17990.28791220.252438653987100
2.1799-2.25780.2781620.235637653927100
2.2578-2.34820.29321500.232738183968100
2.3482-2.4550.2731580.226937913949100
2.455-2.58450.2451480.221438153963100
2.5845-2.74630.29421310.218138513982100
2.7463-2.95830.29661630.207937833946100
2.9583-3.25590.23651730.194237823955100
3.2559-3.72660.2091320.174538343966100
3.7266-4.69380.17511350.146338213956100
4.6938-38.00620.24781250.178838433968100
Refinement TLS params.Method: refined / Origin x: 15.2658 Å / Origin y: 5.2373 Å / Origin z: 21.309 Å
111213212223313233
T0.1646 Å20.0065 Å2-0.0072 Å2-0.1348 Å2-0.0081 Å2--0.1704 Å2
L1.1028 °2-0.1043 °2-0.2665 °2-0.7081 °2-0.0875 °2--1.0512 °2
S0.0531 Å °0.0828 Å °0.0236 Å °-0.1107 Å °-0.0265 Å °0.0783 Å °0.0084 Å °0.1079 Å °-0.0225 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB501
2X-RAY DIFFRACTION1allA6 - 419
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 387

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