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

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Basic information

Entry
Database: PDB / ID: 7qnn
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with inhibitor (surface entropy reduction mutant)
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / P450 / CYP / Tuberculosis / cholesterol / inhibitor / complex / surface / entropy / reduction / cytochrome
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 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-E93 / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsSnee, M. / Tunnicliffe, R. / Leys, D. / Levy, C. / Katariya, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chemistry / Year: 2023
Title: Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis.
Authors: Katariya, M.M. / Snee, M. / Tunnicliffe, R.B. / Kavanagh, M.E. / Boshoff, H.I.M. / Amadi, C.N. / Levy, C.W. / Munro, A.W. / Abell, C. / Leys, D. / Coyne, A.G. / McLean, K.J.
History
DepositionDec 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 2.0Apr 5, 2023Group: Atomic model / Database references ...Atomic model / Database references / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_refine_tls / pdbx_refine_tls_group / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 2.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 2.2Feb 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

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Assembly

Deposited unit
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4543
Polymers46,4891
Non-polymers9652
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-25 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.364, 120.020, 145.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-715-

HOH

21A-718-

HOH

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Components

#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: 46489.078 Da / Num. of mol.: 1 / Mutation: K153A, K332A, K333A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (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]
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-E93 / ethyl 1-(cyclopentylmethyl)-5-pyridin-4-yl-indole-2-carboxylate


Mass: 348.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.55 Å3/Da / Density % sol: 51.85 % / Description: Thin and plate like
Crystal growTemperature: 277.14 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 22% PEG 800, 0.1M Cacodylate pH 5.0, 0.2M Sodium acetate trihydrate.
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.47→145.61 Å / Num. obs: 17538 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 48.66 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.063 / Net I/σ(I): 7.8
Reflection shellResolution: 2.47→2.57 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1 / Num. unique obs: 1939 / CC1/2: 0.849 / Rpim(I) all: 0.453 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IW0

3iw0


Resolution: 2.47→72.81 Å / SU ML: 0.3844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 861 4.93 %
Rwork0.1998 16607 -
obs0.2021 17468 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.94 Å2
Refinement stepCycle: LAST / Resolution: 2.47→72.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 69 121 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373396
X-RAY DIFFRACTIONf_angle_d0.71294631
X-RAY DIFFRACTIONf_chiral_restr0.0425473
X-RAY DIFFRACTIONf_plane_restr0.0053617
X-RAY DIFFRACTIONf_dihedral_angle_d8.1487483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.630.33831330.31682714X-RAY DIFFRACTION99.44
2.63-2.830.3441470.28542701X-RAY DIFFRACTION99.65
2.83-3.110.3241490.26212745X-RAY DIFFRACTION99.69
3.11-3.560.27011360.21532752X-RAY DIFFRACTION99.86
3.56-4.490.21611280.17582805X-RAY DIFFRACTION99.97
4.49-72.810.19941680.15162890X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: -20.3132266852 Å / Origin y: -20.2714824718 Å / Origin z: -18.1207843221 Å
111213212223313233
T0.349229797338 Å2-0.0280726080823 Å20.00625963892764 Å2-0.400958654767 Å2-0.0447258479744 Å2--0.231766148892 Å2
L0.945571054303 °2-0.0206017838639 °2-0.199155070182 °2-1.54788020102 °2-0.383812684036 °2--1.54740179622 °2
S0.0708321441638 Å °-0.0117296871625 Å °0.0773494239584 Å °-0.0720799289279 Å °-0.023225201676 Å °-0.06031146303 Å °-0.202034576045 Å °0.159399540561 Å °-0.0455363857738 Å °
Refinement TLS groupSelection details: all

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