PDB-4z02: Crystal structure of BRD1 in complex with Isoquinoline-3-carboxyl...

ID or keywords:

Entry

Database: PDB / ID: 4z02

Title

Crystal structure of BRD1 in complex with Isoquinoline-3-carboxylic acid

Components

Bromodomain-containing protein 1

Keywords

HISTONE-BINDING PROTEIN / BRPF2 Fragment / BRD1 /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

histone H3-K14 acetyltransferase complex /

regulation of developmental process / MOZ/MORF histone acetyltransferase complex /

regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

DONG, A. / IQBAL, A. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural Genomics Consortium (SGC)

Citation

Journal: to be published
Title: Crystal structure of BRD1 incomplex with Isoquinoline-3-carboxylic acid
Authors: IQBAL, A. / DONG, A. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural Genomics Consortium (SGC)

History

Deposition	Mar 25, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4z02.cif.gz	108 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4z02.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z0/4z02 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z02	HTTPS FTP

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Related structure data

Related structure data	3lyiS S: Starting model for refinement
Similar structure data	3lyi-1 3vya-d 2n87-d 2x4y-1 2hti-d 2kiu-d 1kdx-d 6j7w-2 4l1u-1 5hrx-2 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	#139 - Jul 2011 DNA Methyltransferase similarity (4) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Bromodomain-containing protein 1

B: Bromodomain-containing protein 1

hetero molecules

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

1

A: Bromodomain-containing protein 1

hetero molecules

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

2

B: Bromodomain-containing protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.892, 44.980, 131.020
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bromodomain-containing protein 1 / BR140-like protein / Bromodomain and PHD finger-containing protein 2 Mass: 14251.785 Da / Num. of mol.: 2 / Fragment: UNP residues 925-1049 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRARE2-V2R / References: UniProt: O95696
#2: Chemical	ChemComp-4K8 / isoquinoline-3-carboxylic acid Mass: 173.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₇NO₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 10 / Source method: obtained synthetically
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.37 Å³/Da / Density % sol: 48.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 28% PEG 2K MME, 0.1 M Bis-Tris pH6.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.86→50 Å / Num. obs: 23181 / % possible obs: 99.6 % / Redundancy: 6.6 % / B_iso Wilson estimate: 40.01 Å² / R_merge(I) obs: 0.072 / R_pim(I) all: 0.033 / R_rim(I) all: 0.08 / Χ²: 1.962 / Net I/av σ(I): 41.818 / Net I/σ(I): 10.7 / Num. measured all: 154100

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.86-1.89	5	0.885	1159	0.669	0.436	0.989	0.763	99.9
1.89-1.93	6	0.746	1113	0.779	0.332	0.818	0.815	100
1.93-1.96	6.5	0.617	1160	0.853	0.262	0.671	0.821	100
1.96-2	7.1	0.527	1126	0.917	0.21	0.568	0.865	100
2-2.05	7.2	0.437	1143	0.932	0.174	0.471	0.936	100
2.05-2.09	7.2	0.334	1136	0.96	0.132	0.359	0.959	100
2.09-2.15	7.2	0.261	1153	0.97	0.104	0.281	1.022	100
2.15-2.21	7.2	0.23	1142	0.98	0.092	0.248	1.101	100
2.21-2.27	7.2	0.185	1151	0.983	0.074	0.2	1.221	100
2.27-2.34	7.2	0.161	1148	0.989	0.064	0.173	1.255	100
2.34-2.43	7.2	0.15	1137	0.991	0.06	0.161	1.357	100
2.43-2.52	7.1	0.116	1162	0.994	0.047	0.125	1.434	100
2.52-2.64	7.1	0.106	1156	0.993	0.043	0.115	1.733	100
2.64-2.78	7	0.085	1162	0.996	0.035	0.092	1.804	100
2.78-2.95	6.9	0.074	1157	0.996	0.031	0.08	2.256	100
2.95-3.18	6.8	0.065	1179	0.997	0.027	0.071	2.742	99.9
3.18-3.5	6.5	0.059	1177	0.997	0.025	0.065	3.366	100
3.5-4.01	6.1	0.06	1183	0.995	0.027	0.065	4.778	99.7
4.01-5.05	5.6	0.057	1201	0.995	0.027	0.063	5.573	99.3
5.05-50	5	0.058	1236	0.984	0.03	0.066	6.265	94.7

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
BUSTER	2.10.0	refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LYI

3lyi

Resolution: 1.87→20.76 Å / Cor.coef. F_o:F_c: 0.9334 / Cor.coef. F_o:F_c free: 0.9298 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU R_free Blow DPI: 0.138 / SU R_free Cruickshank DPI: 0.136

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.257	743	3.22 %	RANDOM
R_work	0.2285	22303	-	-
obs	0.2293	23046	99.47 %	-

Displacement parameters

B_iso max: 162.06 Å² / B_iso mean: 53.85 Å² / B_iso min: 24.54 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.1224 Å²	0 Å²	0 Å²
2-	-	-0.948 Å²	0 Å²
3-	-	-	-3.1744 Å²

Refine analyze

Luzzati coordinate error obs: 0.331 Å

Refinement step

Cycle: final / Resolution: 1.87→20.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1713	0	40	96	1849
B_iso mean	-	-	42.83	50.52	-
Num. residues	-	-	-	-	223

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	602	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	30	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	263	HARMONIC	5
X-RAY DIFFRACTION	t_it	1814	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	235	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	2093	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	1814	HARMONIC	1.4	0.011
X-RAY DIFFRACTION	t_angle_deg	2465	HARMONIC	1.6	1.03
X-RAY DIFFRACTION	t_omega_torsion				2.51
X-RAY DIFFRACTION	t_other_torsion				17.07

LS refinement shell

Resolution: 1.87→1.95 Å / Total num. of bins used: 12

	R_factor	Num. reflection	% reflection
R_free	0.2625	87	3.18 %
R_work	0.2462	2648	-
all	0.2467	2735	-
obs	-	-	99.47 %

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	4.7375	1.4448	-0.883	2.0789	0.2987	2.6486	0.0556	-0.0956	0.3571	0.1418	-0.0435	0.0698	-0.1027	-0.2066	-0.0121	-0.1045	0.0171	-0.0147	-0.1169	-0.0332	-0.041	40.9073	45.2742	6.4722
2	0	-0.6826	-0.3129	3.8417	-0.8268	0.1012	0.0558	0.0592	-0.0317	0.026	-0.2533	-0.107	-0.2662	-0.3104	0.1975	0.0277	0.072	-0.0719	0.0231	-0.0176	0.1607	31.6518	52.1704	1.5503
3	4.9951	2.3553	0.795	4.1182	1.0013	3.4537	0.2029	-0.3511	0.0301	0.3565	-0.2007	0.2415	0.0048	-0.3719	-0.0023	-0.0963	0.0194	-0.0084	-0.0798	-0.0132	-0.0276	36.9989	40.9839	7.6567
4	1.4098	-0.7562	-2.0907	2.5033	0.2084	2.1447	-0.0347	-0.1016	0.1276	0.0512	0.1606	-0.5082	-0.0118	0.6621	-0.1259	-0.126	-0.0312	-0.0561	0.0011	-0.0434	0.0203	55.6912	42.9605	3.7026
5	1.1248	-1.5479	1.7066	1.4412	-0.8914	0.7855	-0.0247	0.1706	0.4158	-0.0832	0.1294	0.18	-0.441	0.0952	-0.1048	0.0004	-0.0166	0.0096	-0.1381	0.0447	0.0845	45.532	56.2283	0.1644
6	5.752	5.0081	3.4035	10.4577	3.8373	8.4359	0.0675	-0.2416	0.2186	0.293	-0.1885	-0.199	-0.3945	-0.3418	0.121	0.1092	0.0349	-0.304	-0.1134	-0.0467	-0.0815	59.5322	56.7831	26.4309
7	0.0002	-0.6207	4.1994	2.0951	1.6367	1.2407	-0.059	0.2082	0.3999	-0.1773	0.0224	-0.1571	-0.1635	0.1484	0.0366	0.2249	-0.0367	-0.304	-0.2079	-0.0224	0.0863	67.1803	70.506	27.3415
8	8.5839	5.1137	5.8026	7.0899	1.2292	0.0189	-0.1445	-0.1308	0.5109	0.0902	0.0979	-0.1147	-0.1176	-0.015	0.0466	0.177	0.1155	-0.304	-0.2139	-0.0674	-0.0687	62.1835	61.0594	27.0274
9	4.5774	-1.1725	4.8912	1.8681	0.5758	8.7001	-0.0695	0.037	-0.1239	0.1405	-0.0998	-0.1685	-0.2613	0.1323	0.1693	0.0438	-0.0044	-0.229	-0.1087	-0.0546	-0.15	57.9214	50.8177	20.3012
10	4.9652	-0.3542	-0.3424	2.4746	-0.6749	5.2271	0.1369	-0.2271	-0.2218	0.7421	-0.0698	-0.2506	0.0299	-0.8598	-0.0671	0.1766	-0.0417	-0.2564	0.009	0.0129	-0.1019	56.2662	46.6444	30.773

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|929 - A\|953 }
2	X-RAY DIFFRACTION	2	{ A\|954 - A\|972 }
3	X-RAY DIFFRACTION	3	{ A\|973 - A\|1012 }
4	X-RAY DIFFRACTION	4	{ A\|1013 - A\|1037 }
5	X-RAY DIFFRACTION	5	{ A\|1038 - A\|1047 }
6	X-RAY DIFFRACTION	6	{ B\|930 - B\|967 }
7	X-RAY DIFFRACTION	7	{ B\|968 - B\|980 }
8	X-RAY DIFFRACTION	8	{ B\|981 - B\|999 }
9	X-RAY DIFFRACTION	9	{ B\|1000 - B\|1020 }
10	X-RAY DIFFRACTION	10	{ B\|1021 - B\|1047 }

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