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- PDB-7zlt: Crystal structure of CYP125 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7zlt
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / cholesterol / tuberculosis / Cytochrome / heme / oxidase / monooxygenase / CYP125
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / biological process involved in interaction with host / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-JFI / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSnee, M. / Kavanagh, M. / Levy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
Authors: Snee, M. / Kavanagh, M.
History
DepositionApr 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 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
B: Steroid C26-monooxygenase
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,19624
Polymers139,9903
Non-polymers4,20621
Water10,719595
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9297
Polymers46,6631
Non-polymers1,2666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0868
Polymers46,6631
Non-polymers1,4227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1829
Polymers46,6631
Non-polymers1,5188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.973, 68.440, 144.458
Angle α, β, γ (deg.)90.000, 93.835, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Steroid C26-monooxygenase / Cholest-4-en-3-one 26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25S)-3-oxocholest-4-en- ...Cholest-4-en-3-one 26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / Cholesterol C26-monooxygenase / Cholesterol C26-monooxygenase [(25S)-3beta-hydroxycholest-5-en-26-oate forming] / Cytochrome P450 125 / Steroid C27-monooxygenase


Mass: 46663.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp125, cyp125A1, Rv3545c, MTCY03C7.11 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WPP1, cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 5 types, 616 molecules

#2: Chemical ChemComp-JFI / ~{N}-(2-morpholin-4-ylethyl)-4-(pyridin-4-ylmethyl)benzamide


Mass: 325.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H23N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.44 Å3/Da / Density % sol: 49.5 % / Description: large "chunky" and rock-like
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1M MES pH 6.2, 1.9M Ammonium Sulphate / Temp details: 4C

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.9→67.83 Å / Num. obs: 104257 / % possible obs: 99.63 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4874 / CC1/2: 0.523 / Rpim(I) all: 0.606 / % possible all: 95.03

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XN8

2xn8


Resolution: 1.9→61.11 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 5032 4.83 %
Rwork0.1836 99104 -
obs0.1853 104136 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9647 0 272 595 10514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007410539
X-RAY DIFFRACTIONf_angle_d0.851314416
X-RAY DIFFRACTIONf_chiral_restr0.04661470
X-RAY DIFFRACTIONf_plane_restr0.00861911
X-RAY DIFFRACTIONf_dihedral_angle_d12.78721492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.2921530.27732980X-RAY DIFFRACTION92.28
1.92-1.940.31031640.27153310X-RAY DIFFRACTION99.48
1.94-1.970.30561700.26773250X-RAY DIFFRACTION99.39
1.97-1.990.29031480.26563311X-RAY DIFFRACTION99.25
1.99-2.020.28471690.2713302X-RAY DIFFRACTION99.68
2.02-2.050.31851680.26353264X-RAY DIFFRACTION99.28
2.05-2.070.29251980.25233281X-RAY DIFFRACTION99.74
2.07-2.110.28791340.23663260X-RAY DIFFRACTION99.36
2.11-2.140.27661440.22483342X-RAY DIFFRACTION99.49
2.14-2.170.27711720.20983296X-RAY DIFFRACTION99.86
2.17-2.210.24431620.20373298X-RAY DIFFRACTION99.91
2.21-2.250.25121710.19433302X-RAY DIFFRACTION99.88
2.25-2.290.25881740.18563309X-RAY DIFFRACTION99.91
2.29-2.340.22441860.18893265X-RAY DIFFRACTION99.83
2.34-2.390.22211920.19213294X-RAY DIFFRACTION99.74
2.39-2.450.1981550.19633350X-RAY DIFFRACTION99.89
2.45-2.510.25951630.19843270X-RAY DIFFRACTION99.83
2.51-2.580.26351570.20373328X-RAY DIFFRACTION99.91
2.58-2.650.24071750.20243323X-RAY DIFFRACTION99.91
2.65-2.740.23591650.19923334X-RAY DIFFRACTION99.94
2.74-2.840.21011800.18483312X-RAY DIFFRACTION99.94
2.84-2.950.23351920.19233274X-RAY DIFFRACTION99.94
2.95-3.080.21911520.20663339X-RAY DIFFRACTION99.94
3.08-3.250.25051560.20573339X-RAY DIFFRACTION99.91
3.25-3.450.19741890.17433329X-RAY DIFFRACTION99.89
3.45-3.720.20041520.16163318X-RAY DIFFRACTION99.97
3.72-4.090.16061650.14373357X-RAY DIFFRACTION99.94
4.09-4.680.15891820.12913347X-RAY DIFFRACTION99.86
4.68-5.90.20021560.16093385X-RAY DIFFRACTION99.58
5.9-61.110.23451880.17963435X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 29.8049015074 Å / Origin y: -4.57386081274 Å / Origin z: 37.6874077252 Å
111213212223313233
T0.286976197861 Å20.00704161662012 Å2-0.0167040834121 Å2-0.255344371714 Å20.0308171658741 Å2--0.3166263151 Å2
L0.13330323602 °2-0.0758994212458 °2-0.354292842979 °2-0.201223698935 °20.241162011094 °2--1.17486451378 °2
S-0.0348411257045 Å °-0.00355010013266 Å °-0.021940550255 Å °-0.0996826222372 Å °0.00252660921256 Å °-0.00668159861092 Å °0.075361514294 Å °0.0745903473606 Å °0.0325595460177 Å °
Refinement TLS groupSelection details: all

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