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- PDB-7smz: X-ray crystal structure of CYP142A3 from Mycobacterium Marinum in... -

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Basic information

Entry
Database: PDB / ID: 7smz
TitleX-ray crystal structure of CYP142A3 from Mycobacterium Marinum in complex with 4-cholesten-3-one
ComponentsCytochrome P450 142A3
KeywordsOXIDOREDUCTASE / substrate bound
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 / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE / Putative cytochrome P450 142
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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
DepositionOct 27, 2021Deposition 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,46918
Polymers90,9032
Non-polymers2,56716
Water7,746430
1
A: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7128
Polymers45,4511
Non-polymers1,2607
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,75810
Polymers45,4511
Non-polymers1,3069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.313, 50.395, 82.577
Angle α, β, γ (deg.)82.320, 75.590, 72.050
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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 (bacteria) / Strain: ATCC BAA-535 / Gene: cyp142, MMRN_53720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5YMP0

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Non-polymers , 5 types, 446 molecules

#2: Chemical ChemComp-K2B / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE


Mass: 384.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate Trihydrate pH= 6.5, 0.2M Sodium Acetate Trihydrate, 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: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.04→47.85 Å / Num. obs: 46798 / % possible obs: 98 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 13.6 / Num. measured all: 166704 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.04-2.090.2881162434210.9280.1820.3423.896.5
9.11-47.850.02918085280.9990.0180.03432.497.6

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Processing

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

2yoo


Resolution: 2.04→46.69 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1989 4.25 %
Rwork0.1799 44781 -
obs0.1818 46770 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.69 Å2 / Biso mean: 28.7293 Å2 / Biso min: 10.64 Å2
Refinement stepCycle: final / Resolution: 2.04→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 178 430 6842
Biso mean--27.54 32.95 -
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046562
X-RAY DIFFRACTIONf_angle_d1.2498925
X-RAY DIFFRACTIONf_dihedral_angle_d26.906927
X-RAY DIFFRACTIONf_chiral_restr0.125978
X-RAY DIFFRACTIONf_plane_restr0.0041183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.090.26951500.22253156330696
2.09-2.140.27871350.20863146328197
2.14-2.210.27051290.19653207333697
2.21-2.280.26041530.19853192334598
2.28-2.360.2481440.19063166331098
2.36-2.450.27881440.19463191333598
2.45-2.570.26541420.19493216335898
2.57-2.70.25161410.19663184332598
2.7-2.870.23831360.19523203333998
2.87-3.090.25871460.18653220336698
3.09-3.40.22161460.18383229337599
3.4-3.90.17161390.15963236337599
3.9-4.910.19071440.15073213335799
4.91-46.690.19931400.17283222336299

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