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- PDB-8a9p: Crystal structure of CYP142 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 8a9p
TitleCrystal structure of CYP142 from Mycobacterium tuberculosis in complex with a fragment
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / cholesterol / Cyp142 / monooxygenase / cytochrome / tuberculosis / mycobacterium
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
BROMIDE ION / (3-phenyl-1,2,4-oxadiazol-5-yl)methanamine / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSnee, M. / Katariya, M. / Levy, C. / Leys, D.
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 a fragment
Authors: Snee, M. / Katariya, M.
#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.
History
DepositionJun 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 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
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3858
Polymers44,3711
Non-polymers1,0137
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-69 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.395, 66.503, 129.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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: 44371.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Plasmid: pET21a / 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]

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Non-polymers , 5 types, 338 molecules

#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-ENK / (3-phenyl-1,2,4-oxadiazol-5-yl)methanamine


Mass: 175.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium Acetate pH4.5, 8% PEG 20,000 , 8% PEG 550MME, 0.25M KBr.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 4C / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→66.5 Å / Num. obs: 60601 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 13.9
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.412 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2955 / CC1/2: 0.705 / Rpim(I) all: 0.613 / % possible all: 98.76

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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: 1.63→42.56 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 2982 4.94 %
Rwork0.1807 57375 -
obs0.1816 60357 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.12 Å2
Refinement stepCycle: LAST / Resolution: 1.63→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 61 331 3478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653250
X-RAY DIFFRACTIONf_angle_d0.77184432
X-RAY DIFFRACTIONf_chiral_restr0.0444487
X-RAY DIFFRACTIONf_plane_restr0.0086590
X-RAY DIFFRACTIONf_dihedral_angle_d7.3643468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.39341370.37222661X-RAY DIFFRACTION98.49
1.66-1.680.38871530.33992664X-RAY DIFFRACTION99.72
1.68-1.720.32121450.32392699X-RAY DIFFRACTION99.75
1.72-1.750.36351580.28552677X-RAY DIFFRACTION99.68
1.75-1.780.26451340.26542705X-RAY DIFFRACTION99.75
1.78-1.820.28911580.25662676X-RAY DIFFRACTION99.89
1.82-1.870.25441450.2542714X-RAY DIFFRACTION99.86
1.87-1.910.26391510.2392711X-RAY DIFFRACTION99.86
1.91-1.960.26191320.21192712X-RAY DIFFRACTION99.89
1.96-2.020.21161370.19732736X-RAY DIFFRACTION100
2.02-2.090.20491160.19082742X-RAY DIFFRACTION99.93
2.09-2.160.21331520.17232711X-RAY DIFFRACTION99.97
2.16-2.250.2151280.17372726X-RAY DIFFRACTION100
2.25-2.350.17971340.16042760X-RAY DIFFRACTION99.93
2.35-2.470.19231530.1652738X-RAY DIFFRACTION100
2.47-2.630.2031440.1712734X-RAY DIFFRACTION99.97
2.63-2.830.18881450.1742745X-RAY DIFFRACTION100
2.83-3.120.18421510.1772760X-RAY DIFFRACTION99.97
3.12-3.570.20591270.17452807X-RAY DIFFRACTION100
3.57-4.490.16081430.14692827X-RAY DIFFRACTION100
4.49-42.560.17651390.17952870X-RAY DIFFRACTION96.6
Refinement TLS params.Method: refined / Origin x: 15.3853043832 Å / Origin y: 45.3596311019 Å / Origin z: 82.3839715146 Å
111213212223313233
T0.321448809873 Å20.00433997780759 Å2-0.0208495815179 Å2-0.246669410731 Å20.0289490128514 Å2--0.183709001753 Å2
L0.98842971877 °20.0535444970605 °2-0.276489836331 °2-0.832335395561 °2-0.221947135307 °2--1.11523080756 °2
S-0.0724297999629 Å °0.148945921721 Å °-0.0182202347169 Å °0.0416866121271 Å °0.0189852514728 Å °-0.0283142397467 Å °0.0653082088944 Å °0.196608703431 Å °0.0474152118479 Å °
Refinement TLS groupSelection details: all

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