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- PDB-7tlo: X-ray crystal structure of substrate free cytochrome P450 CYP142A... -

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Basic information

Entry
Database: PDB / ID: 7tlo
TitleX-ray crystal structure of substrate free cytochrome P450 CYP142A3 from Mycobacterium Marinum
ComponentsCytochrome P450 142A3
KeywordsOXIDOREDUCTASE / 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, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450 142
Similarity search - Component
Biological speciesMycobacterium marinum ATCC BAA-535 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGhith, A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103970 Australia
CitationJournal: Acs Infect Dis. / Year: 2022
Title: The Structures of the Steroid Binding CYP142 Cytochrome P450 Enzymes from Mycobacterium ulcerans and Mycobacterium marinum.
Authors: Ghith, A. / Doherty, D.Z. / Bruning, J.B. / Russell, R.A. / De Voss, J.J. / Bell, S.G.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 142A3
B: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2546
Polymers90,9032
Non-polymers1,3514
Water16,141896
1
A: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1273
Polymers45,4511
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1273
Polymers45,4511
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.406, 101.554, 70.013
Angle α, β, γ (deg.)90.000, 110.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 142A3 / CYP142A3


Mass: 45451.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum ATCC BAA-535 (bacteria)
Strain: ATCC BAA-535 / Gene: cyp142, MMRN_53720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5YMP0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Sodium Cacodylate Trihdyrate pH 6.5, 0.2M Sodium Acetate Trihdrate, 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.55→46.17 Å / Num. obs: 110811 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 11.9 / Num. measured all: 777196 / Scaling rejects: 70
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
1.55-1.5871.2663863554960.7120.5111.3671.6100
8.49-46.176.90.03349067110.9990.0130.03638.499.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKR

2xkr


Resolution: 1.55→36.31 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 5648 5.1 %
Rwork0.1777 105112 -
obs0.1795 110760 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.13 Å2 / Biso mean: 26.5953 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 1.55→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 94 896 7172
Biso mean--17.89 34.84 -
Num. residues----791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.570.32411700.286535133683
1.57-1.590.29271580.275235463704
1.59-1.610.25911900.253334803670
1.61-1.630.30321920.252335093701
1.63-1.650.30662030.246434583661
1.65-1.670.26051700.235735143684
1.67-1.690.26381860.230734763662
1.69-1.720.29092070.228735223729
1.72-1.750.26781810.217434443625
1.75-1.770.26351880.215935063694
1.77-1.80.25521910.21434933684
1.8-1.840.29071970.207534773674
1.84-1.870.26161930.202234893682
1.87-1.910.24281950.205534753670
1.91-1.950.22751880.193435613749
1.95-20.24342040.193134573661
2-2.050.24721740.191834723646
2.05-2.10.22352070.186734933700
2.1-2.170.1911910.176435223713
2.17-2.240.21181880.176434733661
2.24-2.320.21582050.17434813686
2.32-2.410.20891890.17735223711
2.41-2.520.21991840.183335083692
2.52-2.650.23151770.176435203697
2.65-2.820.21241820.180635163698
2.82-3.030.20732040.177834913695
3.03-3.340.19671860.166935163702
3.34-3.820.20381840.153235303714
3.82-4.810.16541750.139135633738
4.81-36.310.17621890.155935853774

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