PDB-6t0f: Crystal structure of CYP124 in complex with cholest-4-en-3-one

ID or keywords:

Entry

Database: PDB / ID: 6t0f

Title

Crystal structure of CYP124 in complex with cholest-4-en-3-one

Components

Methyl-branched lipid omega-hydroxylase

Keywords

OXIDOREDUCTASE / Cytochrome / P450 / CYP / CYP124 / 124 / cholestenone / cholest-4-en-3-one / tuberculosis / mycobacterium tuberculosis

Function / homology

Function and homology information

methyl-branched lipid omega-hydroxylase / methyl-branched fatty acid metabolic process / cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / fatty acid omega-oxidation / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / NADPH binding / iron ion binding / heme binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Bukhdruker, S. / Marin, E. / Varaksa, T. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.

Funding support

Russian Federation, 1items

Citation

Journal: J.Mol.Biol. / Year: 2021
Title: Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis.
Authors: Varaksa, T. / Bukhdruker, S. / Grabovec, I. / Marin, E. / Kavaleuski, A. / Gusach, A. / Kovalev, K. / Maslov, I. / Luginina, A. / Zabelskii, D. / Astashkin, R. / Shevtsov, M. / Smolskaya, S. ...

History

Deposition	Oct 3, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 14, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 13, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2	Feb 3, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0	Feb 17, 2021	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / citation ...atom_site / citation / pdbx_nonpoly_scheme / struct_site_gen Item: _atom_site.auth_seq_id / _citation.year ..._atom_site.auth_seq_id / _citation.year / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6t0f_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	6t0f_full_validation.pdf.gz	2.8 MB	Display
Data in XML	6t0f_validation.xml.gz	96.8 KB	Display
Data in CIF	6t0f_validation.cif.gz	149.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t0/6t0f ftp://data.pdbj.org/pub/pdb/validation_reports/t0/6t0f	HTTPS FTP

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Related structure data

Related structure data	6t0gC 6t0hC 6t0kC 6t0lC 2wm5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2zbz-d 3p3l-1 2z36-2 6zi7-2 3iqd-d 1cle-2 5wrq-1 5fv4-5 6kog-1 3a4z-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (1)

Deposited unit

A: Methyl-branched lipid omega-hydroxylase

B: Methyl-branched lipid omega-hydroxylase

C: Methyl-branched lipid omega-hydroxylase

D: Methyl-branched lipid omega-hydroxylase

hetero molecules

202 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyl-branched lipid omega-hydroxylase

hetero molecules

defined by author
50.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Methyl-branched lipid omega-hydroxylase

hetero molecules

defined by author
50.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Methyl-branched lipid omega-hydroxylase

hetero molecules

defined by author
50.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Methyl-branched lipid omega-hydroxylase

hetero molecules

defined by author
50.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.670, 81.270, 155.850
Angle α, β, γ (deg.)	90.000, 107.286, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Methyl-branched lipid omega-hydroxylase / 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 124 / Steroid C26-monooxygenase / Steroid C27-monooxygenase Mass: 48868.957 Da / Num. of mol.: 4 / Mutation: A65T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: cyp124, Rv2266, MTCY339.44c / Production host: Escherichia coli (E. coli) References: UniProt: P9WPP3, methyl-branched lipid omega-hydroxylase, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]

#1: Protein

Methyl-branched lipid omega-hydroxylase / Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4- ...

Mass: 48868.957 Da / Num. of mol.: 4 / Mutation: A65T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: cyp124, Rv2266, MTCY339.44c / Production host:

Escherichia coli (E. coli)
References: UniProt: P9WPP3, methyl-branched lipid omega-hydroxylase, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 6 types, 2621 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#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-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2591 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 27% PEG 3350, 0.1M MOPS

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 1.033 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.033 Å / Relative weight: 1

Reflection

Resolution: 1.49→50 Å / Num. obs: 360719 / % possible obs: 99.2 % / Redundancy: 10.1 % / B_iso Wilson estimate: 21.89 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.172 / Net I/σ(I): 8.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
6.66-50	9.9	37	4182	1	0.037	97.9
4.71-6.66	9.6	34.1	7569	0.999	0.051	99.8
3.85-4.71	10	36	9710	0.999	0.052	99.8
3.33-3.85	9	29.5	11465	0.998	0.065	99.5
2.98-3.33	9.9	25.4	12949	0.998	0.085	99.8
2.72-2.98	10.4	20.4	14325	0.997	0.111	99.8
2.52-2.72	10.6	16.3	15559	0.995	0.144	99.8
2.36-2.52	9.5	12.3	16682	0.991	0.184	99.7
2.22-2.36	10.3	10.3	17721	0.988	0.233	99.7
2.11-2.22	10.5	8.1	18708	0.981	0.302	99.7
2.01-2.11	10.6	6.2	19699	0.967	0.396	99.6
1.92-2.01	9.7	4.2	20548	0.931	0.553	99.5
1.85-1.92	10	3	21308	0.87	0.764	99.3
1.78-1.85	10.3	2.3	22246	0.811	0.967	99.2
1.72-1.78	10.5	1.73	22871	0.737	1.246	99.1
1.67-1.72	10.5	1.23	23734	0.593	1.692	98.9
1.62-1.67	9.5	0.84	24301	0.403	2.244	98.8
1.57-1.62	10.1	0.69	25093	0.357	2.663	98.6
1.53-1.57	10.3	0.48	25704	0.226	3.485	98.5
1.49-1.53	10.4	0.36	26345	0.136	4.341	98.3

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Processing

Software

Name	Version	Classification
MxCuBE	2	data collection
XDS	20171218	data reduction
XSCALE	20171218	data scaling
PHASER	2.8.3	phasing
PHENIX	1.16_3549	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WM5

2wm5

Resolution: 1.65→29.75 Å / SU ML: 0.1918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1846	13343	5 %	RANDOM
R_work	0.1518	253270	-	-
obs	0.1534	266613	99.45 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 28.39 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→29.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13581	0	456	2591	16628

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0119	16079
X-RAY DIFFRACTION	f_angle_d	1.2287	22178
X-RAY DIFFRACTION	f_chiral_restr	0.0731	2343
X-RAY DIFFRACTION	f_plane_restr	0.008	2976
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9701	9631

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.65-1.67	0.3347	442	0.3021	8334	X-RAY DIFFRACTION	98.74
1.67-1.69	0.3029	438	0.2811	8366	X-RAY DIFFRACTION	98.81
1.69-1.71	0.2943	434	0.2705	8367	X-RAY DIFFRACTION	98.9
1.71-1.73	0.298	449	0.2657	8418	X-RAY DIFFRACTION	98.96
1.73-1.75	0.2655	440	0.2498	8309	X-RAY DIFFRACTION	99.05
1.75-1.78	0.2463	432	0.2358	8423	X-RAY DIFFRACTION	99.2
1.78-1.8	0.2801	445	0.2189	8411	X-RAY DIFFRACTION	99.19
1.8-1.83	0.2509	445	0.2119	8360	X-RAY DIFFRACTION	99.2
1.83-1.86	0.2231	438	0.2017	8357	X-RAY DIFFRACTION	99.33
1.86-1.89	0.2417	436	0.1993	8434	X-RAY DIFFRACTION	99.37
1.89-1.92	0.2294	440	0.1975	8363	X-RAY DIFFRACTION	99.33
1.92-1.96	0.2403	452	0.193	8452	X-RAY DIFFRACTION	99.39
1.96-1.99	0.2193	449	0.177	8436	X-RAY DIFFRACTION	99.56
1.99-2.03	0.1961	446	0.1668	8429	X-RAY DIFFRACTION	99.7
2.03-2.08	0.1907	448	0.153	8424	X-RAY DIFFRACTION	99.63
2.08-2.13	0.1912	446	0.1474	8424	X-RAY DIFFRACTION	99.61
2.13-2.18	0.1795	448	0.1454	8451	X-RAY DIFFRACTION	99.71
2.18-2.24	0.1755	444	0.1411	8419	X-RAY DIFFRACTION	99.76
2.24-2.31	0.1681	443	0.143	8467	X-RAY DIFFRACTION	99.76
2.31-2.38	0.1817	440	0.1375	8484	X-RAY DIFFRACTION	99.62
2.38-2.46	0.1809	453	0.1427	8452	X-RAY DIFFRACTION	99.69
2.46-2.56	0.1816	445	0.1382	8453	X-RAY DIFFRACTION	99.65
2.56-2.68	0.163	440	0.1349	8498	X-RAY DIFFRACTION	99.81
2.68-2.82	0.1847	443	0.1418	8476	X-RAY DIFFRACTION	99.84
2.82-3	0.1698	447	0.1426	8496	X-RAY DIFFRACTION	99.72
3-3.23	0.1644	450	0.1397	8502	X-RAY DIFFRACTION	99.81
3.23-3.55	0.1609	451	0.1361	8487	X-RAY DIFFRACTION	99.59
3.55-4.07	0.166	451	0.1278	8549	X-RAY DIFFRACTION	99.68
4.07-5.12	0.1478	446	0.115	8588	X-RAY DIFFRACTION	99.92
5.12-29.75	0.1667	462	0.1477	8641	X-RAY DIFFRACTION	98.99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.669565460132	0.165170420337	-0.197768236684	1.17643923247	-0.0590534666148	0.420455435152	-0.00624271657788	-0.0282907172323	0.0186001415414	-0.000575762720935	0.0020719046461	-0.0883152901673	-0.00165471016375	0.00454300016094	0.00779883567689	0.178048760603	0.0130916356491	-0.0150392344773	0.170849628299	-0.0140398203159	0.186804229534	18.313475936	44.2116001664	7.63877622986
2	0.650272136949	0.084807385219	0.0344310135573	1.3321744884	0.151734111757	0.972374925929	0.0132635601012	-0.0807576374108	0.0390433900364	0.224200448363	-0.0153933103846	-0.0519378767304	-0.0646297118244	0.0085700663381	0.00677472220006	0.179302808306	0.0120980051598	-0.000195249299996	0.176708090675	-0.0202345606562	0.143378632738	15.8957351769	47.9570170101	22.3550762722
3	0.676056337228	0.123997585588	-0.127918876243	1.61142123824	-0.16436191141	0.467082900096	-0.0128125092245	0.0413330550827	-0.0437903726495	-0.0622767394123	0.00957235442327	-0.140365411184	0.0624082294408	-0.00425154989705	0.013222159051	0.179081198218	0.00590643529205	-0.00751339651908	0.169330619928	-0.0235401899147	0.171427958612	18.5906358196	37.6083594149	8.24121108903
4	0.581515388819	0.136469527686	-0.26866499939	0.92724698798	0.0278587174735	1.04698495673	-0.0303651089694	0.00689635727514	0.0505314709263	-0.0678868327578	-0.0386112715972	0.151330871062	-0.0313411785711	-0.0778369574124	0.0558010914369	0.160693933418	0.0195773050208	-0.0170306378347	0.156405800385	-0.0168492736126	0.208625473914	62.7789809839	44.2538670982	8.17210804456
5	0.841558795922	0.390814463801	0.0509577922603	2.05745424754	0.76394850206	1.39591915235	-0.00355755746948	-0.0925441621509	0.0350976124385	0.0963365485292	-0.076726535549	0.0750357979399	-0.0897355725927	-0.0013526593371	0.0907464718142	0.17314445181	0.00860147840197	0.0263940441622	0.223521881035	-0.0272037430338	0.20121924505	63.1648835192	47.6881957108	22.3185930723
6	0.820224483622	0.280071471004	-0.214082735896	1.23609351879	0.0556847861916	0.732013134107	-0.0377989169771	-0.0042049042578	-0.0303791285638	-0.0563014353666	-0.055351914015	0.106823397183	0.032182001308	-0.0849846030259	0.0953714563099	0.152637934211	0.00944399497041	-0.00147212848739	0.170742638544	-0.0261393356028	0.182518649669	63.2533794075	37.7039512691	8.63465795084
7	0.632042120218	-0.0826465946784	0.347431525572	0.82689647085	-0.137848297528	0.827185160552	0.000708314411521	0.0156662540975	-0.0334309144524	0.00729271440117	-0.0213496045544	0.0189636354193	0.0261938899917	0.0118233538564	0.0184563913619	0.166185499861	-0.0131633607172	0.0171581079685	0.177002797207	-0.0151857304108	0.187886906622	40.3461180142	56.6537932936	65.9143927682
8	1.2857205995	0.140203459788	-0.585438985814	1.47671707397	-0.249990232493	2.26328745099	0.0307634978553	0.147028590841	-0.103984176671	-0.214728301903	0.00792078728553	-0.0248345421657	0.188607016497	0.125072192371	-0.0156112987865	0.201313625363	0.0169491058008	-0.00642327579587	0.204317590438	-0.0562538153387	0.159891270337	41.9735384099	46.1865482248	48.6068687062
9	0.837092850048	-0.13779254286	0.284387615942	1.0109475205	-0.0807944042363	0.600788061965	-0.0158262466141	0.00922148971249	0.0460940145412	0.00435241230375	-0.0287258349092	-0.0176506975506	-0.0348016980468	0.00488973344294	0.0473653566993	0.160298380322	-0.0043623077559	0.00922753520982	0.18717304712	-0.0148466450629	0.170591731543	39.7506400816	63.4779164005	63.8488918061
10	0.422121831686	-0.040370130382	0.177148009519	0.65341307319	-0.0784038177035	0.520516040953	0.00551256369663	-0.067910645227	-0.00113255048273	0.0769098773916	0.00359016698261	0.0258764808637	0.00197485708298	0.00322987893183	-0.006774710754	0.136413789693	-0.00933552352121	0.011284034406	0.147131395834	-0.0107640969255	0.151659211797	-3.11438448153	55.6457092375	70.2158717031
11	0.893592416795	-0.315161481204	0.0582946739558	1.20219574641	0.0377304408916	0.88465126744	0.0405898776478	0.124090412981	-0.0396315430611	-0.198777569437	-0.0578774433377	0.133126921394	0.0393941922438	-0.0723108253034	0.019637883224	0.215810857719	-0.00985537935512	-0.0251441401476	0.21549795918	-0.0307624268464	0.168709062781	-9.82511076041	51.7820610632	48.0057690972
12	0.912828103472	-0.0678858149837	0.289825238442	1.03627978351	-0.00950998138541	0.539106866956	0.0104237024324	0.000594588792771	0.0693210087945	-0.014902180507	-0.0081660926225	-0.00793689169923	-0.0318514580928	0.00685995679696	0.00152580248719	0.161618450213	-0.00508276496237	0.0123668312316	0.181093121023	-0.0130283000283	0.175082155724	-4.96584362633	62.9576235101	62.7814769584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -2:156)
2	X-RAY DIFFRACTION	2	(chain A and resid 157:300)
3	X-RAY DIFFRACTION	3	(chain A and resid 301:428)
4	X-RAY DIFFRACTION	4	(chain B and resid -1:164)
5	X-RAY DIFFRACTION	5	(chain B and resid 165:300)
6	X-RAY DIFFRACTION	6	(chain B and resid 301:428)
7	X-RAY DIFFRACTION	7	(chain C and resid -1:173)
8	X-RAY DIFFRACTION	8	(chain C and resid 174:250)
9	X-RAY DIFFRACTION	9	(chain C and resid 251:428)
10	X-RAY DIFFRACTION	10	(chain D and resid -2:133)
11	X-RAY DIFFRACTION	11	(chain D and resid 134:245)
12	X-RAY DIFFRACTION	12	(chain D and resid 246:428)

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