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- PDB-8a6w: Crystal structure of CYP142 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 8a6w
TitleCrystal structure of CYP142 from Mycobacterium tuberculosis in complex with cholestenone
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / cholestenone / complex / CYP142 / tuberculosis / cholesterol / Cytochrome / monooxygenase / hydroxylase / heme / enzyme
Function / homology
Function and homology information


cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / peptidoglycan-based cell wall / 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
PROTOPORPHYRIN IX CONTAINING FE / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSnee, M. / Amadi, C. / Levy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Citation
Journal: To Be Published
Title: Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with cholestenone
Authors: Snee, M. / Amadi, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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
B: Steroid C26-monooxygenase
E: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2366
Polymers93,2332
Non-polymers2,0024
Water9,044502
1
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6183
Polymers46,6171
Non-polymers1,0012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6183
Polymers46,6171
Non-polymers1,0012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.810, 128.130, 146.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11E-509-

HOH

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Components

#1: Protein Steroid C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4- ...Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / Cholesterol C26-monooxygenase / Cholesterol C26-monooxygenase [(25R)-3beta-hydroxycholest-5-en-26-oate forming] / Cytochrome P450 142 / Steroid C27-monooxygenase


Mass: 46616.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WPL5, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]
#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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.09→58.7 Å / Num. obs: 74246 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.38 Å2 / Rrim(I) all: 0.224 / Net I/σ(I): 6
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5417 / Rrim(I) all: 1.464 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKR

2xkr


Resolution: 2.09→58.7 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.9668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 3629 4.89 %
Rwork0.2011 70538 -
obs0.2028 74167 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.34 Å2
Refinement stepCycle: LAST / Resolution: 2.09→58.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 142 502 6816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256463
X-RAY DIFFRACTIONf_angle_d0.61988811
X-RAY DIFFRACTIONf_chiral_restr0.0361973
X-RAY DIFFRACTIONf_plane_restr0.0041160
X-RAY DIFFRACTIONf_dihedral_angle_d7.4653905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.33421360.29622728X-RAY DIFFRACTION100
2.12-2.150.32451160.28352655X-RAY DIFFRACTION100
2.15-2.180.33621430.27032673X-RAY DIFFRACTION99.96
2.18-2.210.27981470.25752682X-RAY DIFFRACTION100
2.21-2.240.29421400.25032641X-RAY DIFFRACTION100
2.24-2.280.29871580.2422688X-RAY DIFFRACTION100
2.28-2.320.28141400.2332674X-RAY DIFFRACTION100
2.32-2.360.26681180.22732729X-RAY DIFFRACTION100
2.36-2.410.22241410.21952662X-RAY DIFFRACTION100
2.41-2.460.27161410.21492678X-RAY DIFFRACTION100
2.46-2.510.23941370.21022689X-RAY DIFFRACTION100
2.51-2.570.27171390.20542703X-RAY DIFFRACTION99.93
2.57-2.630.27141410.2142701X-RAY DIFFRACTION99.96
2.63-2.70.21881540.19862668X-RAY DIFFRACTION100
2.7-2.780.24951390.20732706X-RAY DIFFRACTION100
2.78-2.870.27781470.20952697X-RAY DIFFRACTION99.93
2.87-2.980.22741310.21352707X-RAY DIFFRACTION99.89
2.98-3.10.24431430.20822675X-RAY DIFFRACTION99.96
3.1-3.240.25241420.2052716X-RAY DIFFRACTION99.93
3.24-3.410.22931390.20432734X-RAY DIFFRACTION100
3.41-3.620.24741340.19352734X-RAY DIFFRACTION100
3.62-3.90.21351550.16572744X-RAY DIFFRACTION100
3.9-4.290.18071440.15532723X-RAY DIFFRACTION99.9
4.29-4.910.17171430.14772764X-RAY DIFFRACTION99.9
4.91-6.190.21751260.18782827X-RAY DIFFRACTION99.93
6.19-58.70.21381350.20882940X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: 63.8618756903 Å / Origin y: -43.2121126241 Å / Origin z: -37.0058057975 Å
111213212223313233
T0.201279918259 Å2-0.00170780350214 Å2-0.00620115307073 Å2-0.188071980658 Å20.00634477926723 Å2--0.224005278984 Å2
L0.54730889706 °2-0.0158344330615 °2-0.331278802892 °2-0.0810473494377 °20.0369800054162 °2--0.625772183678 °2
S0.0104568257265 Å °-0.000593684326474 Å °0.160897198154 Å °0.000346584350276 Å °-0.0597297673309 Å °-0.00341254279505 Å °-0.0479405017791 Å °-0.000970361013855 Å °0.0462631295906 Å °
Refinement TLS groupSelection details: all

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