PDB-4pkl: Bromodomain of Trypanosoma brucei BDF2 With IBET-151

ID or keywords:

Entry

Database: PDB / ID: 4pkl

Title

Bromodomain of Trypanosoma brucei BDF2 With IBET-151

Components

Bromodomain factor 2

Keywords

SIGNALING PROTEIN/INHIBITOR /

SIGNALING PROTEIN /

INHIBITOR /

HISTONE / EPIGENETIC READER /

SIGNALING PROTEIN-INHIBITOR complex

Function / homology

Function and homology information

lysine-acetylated histone binding /

histone binding /

chromatin remodeling / regulation of transcription by RNA polymerase II /

nucleus
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.251 Å

Authors

Debler, E.W.

Funding support

United States, 1items

Citation

Journal: Plos Biol. / Year: 2015
Title: Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome.
Authors: Schulz, D. / Mugnier, M.R. / Paulsen, E.M. / Kim, H.S. / Chung, C.W. / Tough, D.F. / Rioja, I. / Prinjha, R.K. / Papavasiliou, F.N. / Debler, E.W.

History

Deposition	May 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 16, 2020	Group: Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4pkl.cif.gz	113.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pk/4pkl ftp://data.pdbj.org/pub/pdb/validation_reports/pk/4pkl	HTTPS FTP

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Related structure data

Similar structure data	6c7r-d 1cyv-d 4g4f-d 5syd-1 5lw8-d 3lrg-1 1mak-d 6sru-6 3csp-d 2o9u-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (1)

Deposited unit

A: Bromodomain factor 2

B: Bromodomain factor 2

hetero molecules

28.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bromodomain factor 2

hetero molecules

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

2

B: Bromodomain factor 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.869, 62.091, 62.117
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Bromodomain factor 2 Mass: 13500.117 Da / Num. of mol.: 2 / Fragment: Bromodomain, UNP residues 9-123 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.6k15.3240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38AM1

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Non-polymers , 6 types, 281 molecules

#2: Chemical	ChemComp-1GH / 7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE Mass: 415.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₂₁N₅O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H₂O

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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 Å³/Da / Density % sol: 38.35 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: sodium potassium phosphate pH 6.6, acetate pH 4.1, 1-propanol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.25→50 Å / Num. obs: 60028 / % possible obs: 99.9 % / Redundancy: 7 % / R_sym value: 0.058 / Net I/σ(I): 37.4
Reflection shell	Resolution: 1.25→1.29 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.946 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
ARP		model building
HKL-2000		data reduction
PHASER		phasing
Coot		model building
HKL-2000		data scaling
O		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.251→31.059 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1792	2035	3.4 %
R_work	0.1692	-	-
obs	0.1695	59801	99.11 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.251→31.059 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1741	0	76	274	2091

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1886
X-RAY DIFFRACTION	f_angle_d	1.084	2571
X-RAY DIFFRACTION	f_dihedral_angle_d	13.237	670
X-RAY DIFFRACTION	f_chiral_restr	0.048	273
X-RAY DIFFRACTION	f_plane_restr	0.005	322

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 (%)
1.2508-1.2799	0.2585	102	0.2569	3507	X-RAY DIFFRACTION	91
1.2799-1.3119	0.2364	203	0.2525	3762	X-RAY DIFFRACTION	99
1.3119-1.3473	0.228	103	0.2376	3862	X-RAY DIFFRACTION	99
1.3473-1.387	0.2142	102	0.221	3859	X-RAY DIFFRACTION	100
1.387-1.4318	0.2323	104	0.2129	3827	X-RAY DIFFRACTION	100
1.4318-1.4829	0.1955	201	0.188	3777	X-RAY DIFFRACTION	100
1.4829-1.5423	0.194	103	0.1739	3890	X-RAY DIFFRACTION	100
1.5423-1.6125	0.2096	103	0.1635	3860	X-RAY DIFFRACTION	100
1.6125-1.6975	0.1998	201	0.1657	3797	X-RAY DIFFRACTION	100
1.6975-1.8038	0.2055	102	0.1647	3915	X-RAY DIFFRACTION	100
1.8038-1.9431	0.1963	102	0.1701	3953	X-RAY DIFFRACTION	100
1.9431-2.1386	0.1798	203	0.1589	3809	X-RAY DIFFRACTION	100
2.1386-2.448	0.1817	102	0.158	3943	X-RAY DIFFRACTION	100
2.448-3.0837	0.169	203	0.1682	3896	X-RAY DIFFRACTION	100
3.0837-31.0681	0.1489	101	0.1552	4109	X-RAY DIFFRACTION	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	7.0101	3.8716	3.1263	2.7279	0.9746	2.4046	0.3015	-0.0592	-0.7567	-0.0198	-0.258	0.3133	0.8419	-0.4565	-0.0548	0.2672	-0.0355	-0.0234	0.2221	-0.0028	0.2342	43.4032	28.9071	11.7443
2	1.4878	0.933	-0.4154	3.4107	-1.3067	1.3786	0.0713	-0.0586	0.0998	0.1912	-0.0452	0.0689	-0.099	0.0165	-0.0369	0.1194	0.0022	0.0168	0.1195	-0.0094	0.1121	50.703	46.6509	14.8982
3	5.6437	0.6273	-1.4216	6.8176	0.5192	2.895	0.0753	-0.1568	0.0066	-0.0014	-0.0164	0.4584	-0.447	-0.0486	-0.0682	0.2025	0.0076	-0.0088	0.1906	0.1506	0.3888	48.8548	62.7531	3.3697
4	5.1595	-0.5296	0.6008	5.0291	0.9235	3.0434	-0.0738	0.8922	0.4204	-0.4045	0.2119	0.3531	0.4376	-0.4116	-0.0867	0.2044	-0.034	-0.004	0.2339	0.0607	0.1547	50.5843	52.7114	-1.8317
5	2.2619	1.2318	0.2776	3.4125	-0.0784	1.5083	0.0114	0.0669	0.0209	-0.1057	-0.0241	0.2117	0.002	-0.1351	0.0169	0.1154	-0.0076	-0.0029	0.1266	-0.0049	0.1108	45.5299	39.0511	8.0644
6	1.5585	0.3342	-0.381	3.9568	-0.6955	3.2304	-0	0.001	0.0421	-0.086	-0.0969	-0.1856	0.0823	0.0539	0.0766	0.0665	0.0017	0.0237	0.0842	0.0089	0.1045	60.8141	50.6086	6.9906
7	3.1553	1.0521	2.8667	0.9191	1.4473	3.2418	-0.0479	0.3593	-0.0217	-0.4501	-0.1059	-0.8015	0.2701	0.5067	0.1608	0.1651	0.0239	0.053	0.169	0.0231	0.2206	61.7943	39.3097	10.056
8	4.3694	5.0977	3.8507	8.5223	2.809	5.3919	-0.0957	0.092	-0.285	-0.0079	0.0964	-0.1831	0.2118	0.0137	-0.0047	0.1242	0.0128	0.016	0.1159	-0.0089	0.1183	55.8539	32.2273	15.0871
9	2.7132	-0.1095	1.0955	4.4938	1.1189	4.119	0.0429	-0.5728	0.2342	0.6276	0.0477	-0.2354	-0.2423	0.3201	-0.1013	0.2151	-0.0833	-0.0331	0.2901	0.0008	0.1898	60.681	43.5259	45.4155
10	3.0606	0.7455	-0.7834	4.7618	0.7117	4.6239	0.0649	-0.0838	0.0111	0.1266	-0.0016	-0.1684	-0.0811	0.3229	-0.0188	0.0977	-0.0285	0.0092	0.1231	-0.0011	0.0852	55.8801	41.3003	30.896
11	4.8313	2.4722	0.4464	2.5853	2.628	4.4023	0.703	0.8892	0.6475	-0.4602	0.4578	-0.2307	-1.4016	-0.2524	-0.7284	0.4641	0.1609	0.1433	0.3868	-0.0186	0.4273	42.9906	50.0081	23.8779
12	7.2129	-0.2965	2.1634	5.9462	1.181	2.3318	0.0081	0.1623	0.4079	-0.0618	-0.1394	0.9115	-0.2015	-0.6063	0.0215	0.2253	0.0927	0.0406	0.2808	0.0001	0.3487	37.4794	45.3355	31.3768
13	1.6917	0.2453	0.5569	1.6639	0.3836	2.8029	0.0128	-0.1545	0.1166	0.142	-0.0267	0.0125	-0.2359	-0.0257	0.0277	0.1287	-0.0123	0.0317	0.1215	-0.0095	0.1033	49.4215	39.7954	37.4266
14	4.7051	1.2005	3.9908	2.738	-0.4863	4.3159	0.6618	-0.1333	-1.0809	0.664	-0.3068	-0.2454	0.5941	0.4867	-0.1736	0.289	0.0017	-0.0745	0.2213	0.0346	0.2386	57.608	31.8986	44.595
15	8.0846	-1.8725	-2.7557	6.0566	2.2874	2.1765	0.2876	-0.4763	-0.7491	0.567	-0.343	-0.1549	0.4229	0.0761	0.0656	0.3012	-0.0934	-0.0835	0.3383	0.0613	0.256	59.6376	35.6504	48.2089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 8:12)
2	X-RAY DIFFRACTION	2	(chain A and resid 13:37)
3	X-RAY DIFFRACTION	3	(chain A and resid 38:42)
4	X-RAY DIFFRACTION	4	(chain A and resid 43:51)
5	X-RAY DIFFRACTION	5	(chain A and resid 52:76)
6	X-RAY DIFFRACTION	6	(chain A and resid 77:99)
7	X-RAY DIFFRACTION	7	(chain A and resid 100:104)
8	X-RAY DIFFRACTION	8	(chain A and resid 105:114)
9	X-RAY DIFFRACTION	9	(chain B and resid 9:20)
10	X-RAY DIFFRACTION	10	(chain B and resid 21:34)
11	X-RAY DIFFRACTION	11	(chain B and resid 35:40)
12	X-RAY DIFFRACTION	12	(chain B and resid 41:49)
13	X-RAY DIFFRACTION	13	(chain B and resid 50:103)
14	X-RAY DIFFRACTION	14	(chain B and resid 104:108)
15	X-RAY DIFFRACTION	15	(chain B and resid 109:114)

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