PDB-3lxj: Crystal Structure of the Bromodomain of Human AAA domain containi...

ID or keywords:

Entry

Database: PDB / ID: 3lxj

Title

Crystal Structure of the Bromodomain of Human AAA domain containing 2B (ATAD2B)

Components

ATPase family AAA domain-containing protein 2B

Keywords

HYDROLASE /

ATPase family / AAA domain containing 2B / ATAD2B /

bromodomain /

Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding /

Phosphoprotein

Function / homology

Function and homology information

lysine-acetylated histone binding /

histone binding /

chromatin binding /

ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II /

nucleoplasm /

ATP binding /

nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.33 Å

Authors

Filippakopoulos, P. / Keates, T. / Picaud, S. / Fedorov, O. / Krojer, T. / Vollmar, M. / Muniz, J. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. ...

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.

History

Deposition	Feb 25, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 11, 2012	Group: Database references
Revision 1.3	Jan 31, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lxj.cif.gz	225.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3lxj.ent.gz	185 KB	Display	PDB format
PDBx/mmJSON format	3lxj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lx/3lxj ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lxj	HTTPS FTP

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Related structure data

Related structure data	2nxbSC 2oo1SC 2ossSC 2ouoSC 2rfjSC 3d7cSC 3daiSC 3dwySC 3gg3C 3hmeC 3hmfC 3hmhSC 3i3jC 3iu5C 3iu6C 3mb3C 3mb4C 3mqmC 3nxbC 3p1cC 3p1dC 3q2eC 3rcwC 3tlpC 3uv2C 3uv4C 3uv5C 3uvdC 3uvwC 3uvxC 3uvyC 3uw9C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5qxu-d 6p38-d 6p3a-2 6epj-d 6p3a-1 5r4w-d 5qxs-d 6hic-d 5qxm-d 4qsw-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) 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

2nxbSC

2oo1SC

2ossSC

2ouoSC

2rfjSC

3d7cSC

3daiSC

3dwySC

3hmhSC

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	#80 - Aug 2006 AAA+ Proteases similarity (4) #166 - Oct 2013 Proteasome similarity (4) #167 - Nov 2013 SNARE Proteins similarity (4) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: ATPase family AAA domain-containing protein 2B

B: ATPase family AAA domain-containing protein 2B

C: ATPase family AAA domain-containing protein 2B

D: ATPase family AAA domain-containing protein 2B

hetero molecules

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

1

A: ATPase family AAA domain-containing protein 2B

hetero molecules

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

2

B: ATPase family AAA domain-containing protein 2B

hetero molecules

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

3

C: ATPase family AAA domain-containing protein 2B

hetero molecules

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

4

D: ATPase family AAA domain-containing protein 2B

hetero molecules

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

Unit cell

Length a, b, c (Å)	79.640, 79.640, 204.051
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
1	3	C
2	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	984
2	1	1	5	B	984
3	1	1	5	C	984
4	1	1	5	D	984
1	2	1	5	A	1004 - 1038
2	2	1	5	B	1004 - 1038
3	2	1	5	C	1004 - 1038
4	2	1	5	D	1004 - 1038
1	3	1	4	A	1051 - 1085
2	3	1	4	B	1051 - 1085
3	3	1	4	C	1051 - 1085
4	3	1	4	D	1051 - 1085
1	1	2	5	A	986 - 1002
2	1	2	5	B	986 - 1002
1	1	3	5	C	986 - 1002
2	1	3	5	D	986 - 1002

NCS ensembles :

ID
1
2
3

#1: Protein	ATPase family AAA domain-containing protein 2B Mass: 15834.093 Da / Num. of mol.: 4 / Fragment: Bromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2B, KIAA1240 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9ULI0
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.95 Å³/Da / Density % sol: 58.3 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% isopropanol 0.1M tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9204 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2009

Radiation

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

Radiation wavelength

Wavelength: 0.9204 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.512
1	1	-H-K, K, -L	2	0.488

Reflection

Resolution: 2.327→40.81 Å / Num. all: 31225 / Num. obs: 31006 / % possible obs: 99.3 % / Redundancy: 4.9 % / R_merge(I) obs: 0.08 / R_sym value: 0.08 / Net I/σ(I): 10.8

Reflection shell

Resolution: 2.34→2.46 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.653 / Mean I/σ(I) obs: 2 / R_sym value: 0.653 / % possible all: 99.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 56.03 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	37.09 Å
Translation	2.5 Å	37.09 Å

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Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
CrystalClear		data collection
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY

Resolution: 2.33→40.81 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.482 / SU ML: 0.107 / SU R Cruickshank DPI: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2534	1586	5.2 %	RANDOM
R_work	0.21206	-	-	-
obs	0.21405	29113	98.99 %	-
all	-	31012	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 45.949 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.62 Å²	0 Å²	0 Å²
2-	-	6.62 Å²	0 Å²
3-	-	-	-13.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→40.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4268	0	20	136	4424

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4343
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2978
X-RAY DIFFRACTION	r_angle_refined_deg	1.307	1.985	5863
X-RAY DIFFRACTION	r_angle_other_deg	0.865	3	7282
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.799	5	535
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.432	24.493	207
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.461	15	805
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.132	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	686
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4760
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	827
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.856	3	2707
X-RAY DIFFRACTION	r_mcbond_other	1.21	3	1058
X-RAY DIFFRACTION	r_mcangle_it	3.906	5	4374
X-RAY DIFFRACTION	r_scbond_it	6.334	8	1636
X-RAY DIFFRACTION	r_scangle_it	6.558	11	1489
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	650	medium positional	0.25	0.5
1	1	B	650	medium positional	0.32	0.5
1	1	C	650	medium positional	0.25	0.5
1	1	D	650	medium positional	0.29	0.5
2	2	A	100	medium positional	0.18	0.5
3	3	A	100	medium positional	0.18	0.5
1	1	A	252	loose positional	0.34	5
1	1	B	252	loose positional	0.32	5
1	1	C	252	loose positional	0.33	5
1	1	D	252	loose positional	0.31	5
2	2	A	69	loose positional	0.25	5
3	3	A	97	loose positional	0.32	5
1	1	A	650	medium thermal	0.86	2
1	1	B	650	medium thermal	0.85	2
1	1	C	650	medium thermal	0.9	2
1	1	D	650	medium thermal	0.87	2
2	2	A	100	medium thermal	0.42	2
3	3	A	100	medium thermal	0.68	2
1	1	A	252	loose thermal	1.06	10
1	1	B	252	loose thermal	0.91	10
1	1	C	252	loose thermal	1.07	10
1	1	D	252	loose thermal	0.94	10
2	2	A	69	loose thermal	0.49	10
3	3	A	97	loose thermal	0.89	10

LS refinement shell

Resolution: 2.334→2.395 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	116	-
R_work	0.341	2085	-
obs	-	-	97.39 %

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	11.0146	-3.7229	0.8665	2.8198	-0.8103	1.9754	0.045	0.1444	0.1654	-0.0319	-0.0085	-0.1735	0.0113	-0.0161	-0.0365	0.1709	-0.0606	-0.0297	0.2832	0.0011	0.1244	58.4204	33.3108	27.7725
2	5.8671	1.0994	-4.3035	2.4669	-6.2952	16.4929	-0.2819	-0.0431	-0.7969	-0.6528	-0.2939	-0.129	1.628	0.8399	0.5757	0.6238	0.0326	0.0132	0.5329	0.0118	0.5792	72.5006	11.0551	30.2142
3	1.7612	0.4716	-0.416	1.6485	-0.1503	1.9655	0.0101	-0.3979	-0.5419	0.2093	0.1328	-0.194	0.2964	0.066	-0.1428	0.1265	-0.0032	-0.0362	0.2089	0.0545	0.2582	64.6334	22.8589	35.386
4	10.9988	-1.4387	2.1349	2.6805	-0.8369	1.9741	-0.0706	-0.383	-0.1409	0.3492	0.0632	0.0832	-0.0902	-0.3125	0.0074	0.2465	-0.0077	-0.012	0.378	-0.0043	0.0924	56.0946	35.1603	37.6655
5	5.0873	5.0513	-1.1859	16.3318	-2.9903	3.2497	0.0908	-0.1177	0.0458	0.3231	-0.0227	-0.0716	0.1652	0.0279	-0.0681	0.2007	-0.0442	-0.0113	0.2603	0.0053	0.0767	58.7255	30.6798	68.1084
6	11.0626	-2.2239	1.5801	1.5231	-0.0287	8.001	-0.0343	-0.0134	0.7051	0.0539	0.0412	0.7307	-1.0712	-1.0121	-0.0069	0.571	-0.0209	0.0068	0.4243	0.0934	0.7824	48.6373	52.1587	63.5513
7	1.8501	0.401	-0.3733	4.2199	-0.7391	2.3031	-0.0031	0.1622	0.2966	-0.4135	0.1443	0.2264	0.0231	-0.0138	-0.1412	0.2278	-0.0773	-0.0342	0.24	0.0555	0.2319	56.5499	39.379	59.1836
8	4.2608	-0.1625	-15.3448	0.3652	-1.553	68.001	-0.599	0.1939	0.4279	0.1892	0.277	-0.3391	0.9633	-2.659	0.3221	0.7122	-0.084	-0.1978	0.8668	0.0697	0.5877	44.2333	18.5515	59.9076
9	4.0418	2.0585	-0.587	3.0665	-1.0682	3.8593	0.1475	-0.386	-0.1177	0.066	-0.043	0.1744	0.0304	-0.0455	-0.1046	0.1302	0.0612	-0.0105	0.1008	0.0113	0.0819	17.7569	34.827	47.7402
10	0.1994	1.395	1.0967	32.3638	6.5791	6.1162	-0.037	0.0191	-0.1898	-0.7619	1.0557	-1.9729	-0.4292	0.1155	-1.0188	0.5349	0.0124	-0.1459	0.5136	-0.0116	0.6132	31.069	54.5305	49.7166
11	2.6845	0.3349	-0.993	1.5899	-0.9642	2.1978	-0.0012	0.2155	-0.0049	-0.081	0.0561	0.1006	-0.0822	0.1108	-0.0549	0.1871	0.0877	-0.0361	0.2092	-0.0211	0.1094	23.0131	42.19	39.3218
12	18.1643	-4.6919	-1.4118	13.2614	-16.8113	24.5971	0.6506	-0.8665	3.1369	-0.5568	0.7306	0.0333	0.5445	-0.5222	-1.3811	0.6183	0.1521	-0.0276	0.9519	0.0084	0.8215	-1.6245	40.412	39.794
13	11.8984	-6.5039	-2.5056	12.6616	11.6578	12.1668	0.0578	0.0656	-0.2596	0.1705	0.4703	-0.4513	0.2843	0.466	-0.5281	0.6449	-0.0074	0.1017	0.631	-0.0303	0.6329	29.1311	15.5409	12.4339
14	0.9068	-0.3467	1.0969	3.1803	0.7341	2.2946	0.1044	0.0614	-0.1594	-0.3859	-0.1515	0.5094	-0.2364	-0.2789	0.0471	0.2714	0.0751	-0.0036	0.3456	-0.0097	0.2702	19.1838	37.1003	14.0515
15	10.2123	11.3043	-10.4132	12.8888	-12.2916	12.1809	-0.373	0.0001	0.1629	-0.2336	-0.0681	-0.1236	-0.045	0.1512	0.4411	0.5076	-0.0341	0.0406	0.6941	-0.0401	0.5664	31.5672	54.3342	12.3246
16	1.7929	-0.1918	0.2759	3.1666	0.9724	2.3802	-0.0167	-0.1464	-0.1309	0.1813	0.0736	-0.0795	-0.0776	0.0484	-0.0569	0.1373	0.0285	-0.0049	0.2869	0.0439	0.1017	25.4907	40.003	22.3064

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	951 - 987
2	X-RAY DIFFRACTION	2	A	988 - 995
3	X-RAY DIFFRACTION	3	A	996 - 1048
4	X-RAY DIFFRACTION	4	A	1049 - 1085
5	X-RAY DIFFRACTION	5	B	951 - 980
6	X-RAY DIFFRACTION	6	B	981 - 1003
7	X-RAY DIFFRACTION	7	B	1004 - 1080
8	X-RAY DIFFRACTION	8	B	1081 - 1085
9	X-RAY DIFFRACTION	9	C	951 - 984
10	X-RAY DIFFRACTION	10	C	985 - 991
11	X-RAY DIFFRACTION	11	C	992 - 1080
12	X-RAY DIFFRACTION	12	C	1081 - 1085
13	X-RAY DIFFRACTION	13	D	951 - 957
14	X-RAY DIFFRACTION	14	D	958 - 984
15	X-RAY DIFFRACTION	15	D	985 - 992
16	X-RAY DIFFRACTION	16	D	993 - 1084

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi