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- PDB-7sh5: Crystal structure of CYP142A3 from Mycobacterium ulcerans bound t... -

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Basic information

Entry
Database: PDB / ID: 7sh5
TitleCrystal structure of CYP142A3 from Mycobacterium ulcerans bound to Cholest-4-en-3-one
ComponentsCytochrome P450 142A3
KeywordsLIPID BINDING PROTEIN / OXIDOREDUCTASE / P450 / heme / mono-oxygenase / lipid / catabolism / cholesterol / cholest-4-en-3-one / mycobacteria / tuberculosis / ulcerans
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 / Cytochrome P450 142A3 Cyp142A3
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsDoherty, D.Z. / Bell, S.G. / Bruning, J.
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 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 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
C: Cytochrome P450 142A3
D: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,16732
Polymers181,4504
Non-polymers4,71728
Water29,5811642
1
A: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5749
Polymers45,3621
Non-polymers1,2118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5647
Polymers45,3621
Non-polymers1,2016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5158
Polymers45,3621
Non-polymers1,1527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 142A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5158
Polymers45,3621
Non-polymers1,1527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.685, 59.200, 114.937
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome P450 142A3 / Cyp142A3


Mass: 45362.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: cyp142A3, MUL_4077 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PUV7

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Non-polymers , 5 types, 1670 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K2B / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE


Mass: 384.638 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H44O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1642 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium Acetate pH 5.5-6.0, 10% PEG 8000, 0.1 M Sodium cacodylate trihydrate
PH range: 5.5-6.0

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.83→47.87 Å / Num. obs: 132141 / % possible obs: 98.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Net I/σ(I): 18.2 / Num. measured all: 935212 / Scaling rejects: 7
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
1.83-1.867.20.4594532163380.9140.1820.494396.3
10.02-47.876.70.015593488010.0060.01658.398.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YOO

2yoo


Resolution: 1.83→40.807 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 1991 1.51 %
Rwork0.1695 130118 -
obs0.17 132109 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.26 Å2 / Biso mean: 25.2768 Å2 / Biso min: 8.92 Å2
Refinement stepCycle: final / Resolution: 1.83→40.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12570 0 325 1642 14537
Biso mean--19.63 32.83 -
Num. residues----1590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313262
X-RAY DIFFRACTIONf_angle_d1.18118058
X-RAY DIFFRACTIONf_chiral_restr0.1391983
X-RAY DIFFRACTIONf_plane_restr0.0032377
X-RAY DIFFRACTIONf_dihedral_angle_d9.17711115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.87540.28141310.2104914597
1.8754-1.92610.20991390.197924398
1.9261-1.98280.26491480.2024922599
1.9828-2.04680.22511400.1893925699
2.0468-2.120.24271480.185929699
2.12-2.20480.22691330.1776928599
2.2048-2.30520.18591390.1745930199
2.3052-2.42670.21191460.1735916398
2.4267-2.57870.20571340.1788907496
2.5787-2.77780.19321460.18079348100
2.7778-3.05720.21441500.18299427100
3.0572-3.49940.20211460.17239475100
3.4994-4.40810.18231510.1425945099
4.4081-40.80.15351400.1466943097

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