PDB-2rjc: Crystal structure of L3MBTL1 protein in complex with MES

ID or keywords:

Entry

Database: PDB / ID: 2rjc

Title

Crystal structure of L3MBTL1 protein in complex with MES

Components

Lethal(3)malignant brain tumor-like protein

Keywords

TRANSCRIPTION / L(3)MBT-LIKE PROTEIN /

STRUCTURAL GENOMICS /

STRUCTURAL GENOMICS CONSORTIUM / SGC / Chromatin regulator / DNA-binding / Metal-binding /

Nucleus /

Repressor /

Transcription regulation /

Zinc-finger

Function / homology

Function and homology information

SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division /

hemopoiesis /

nucleosome binding / heterochromatin formation / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. ...

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2007
Title: L3MBTL1 recognition of mono- and dimethylated histones.
Authors: Min, J. / Allali-Hassani, A. / Nady, N. / Qi, C. / Ouyang, H. / Liu, Y. / MacKenzie, F. / Vedadi, M. / Arrowsmith, C.H.

History

Deposition	Oct 14, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	2rjc.cif.gz	219.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2rjc.ent.gz	176.7 KB	Display	PDB format
PDBx/mmJSON format	2rjc.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/rj/2rjc ftp://data.pdbj.org/pub/pdb/validation_reports/rj/2rjc	HTTPS FTP

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Related structure data

Related structure data	2pqwSC 2rjdC 2rjeC 2rjfC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ri3-d 3p8h-2 3oq5-3 2rjf-4 3p8h-1 3p8h-3 2rhi-d 2rhy-d 3oq5-2 2rhz-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2pqwSC

2rjdC

2rjeC

2rjfC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lethal(3)malignant brain tumor-like protein

B: Lethal(3)malignant brain tumor-like protein

C: Lethal(3)malignant brain tumor-like protein

hetero molecules

115 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lethal(3)malignant brain tumor-like protein

hetero molecules

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

2

B: Lethal(3)malignant brain tumor-like protein

hetero molecules

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

3

C: Lethal(3)malignant brain tumor-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.548, 108.784, 90.348
Angle α, β, γ (deg.)	90.00, 90.91, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lethal(3)malignant brain tumor-like protein / L(3)mbt-like / L(3)mbt protein homolog / H-l(3)mbt protein / H-L(3)MBT / L3MBTL1 Mass: 37751.211 Da / Num. of mol.: 3 / Fragment: Residues 200-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pET28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y468
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.76 Å³/Da / Density % sol: 55.39 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 4% PEG 4000, 0.1 M Sodium acetate, 0.1 M MES pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 10, 2006 / Details: varimax
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2→90.17 Å / Num. all: 82054 / Num. obs: 82054 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.088

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CrystalClear		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2PQW

2pqw

Resolution: 2→90.17 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.929 / SU B: 7.5 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24127	4116	5 %	RANDOM
R_work	0.19487	-	-	-
all	0.19718	78050	-	-
obs	0.19718	78050	99.65 %	-

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: 26.048 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.8 Å²	0 Å²	0.15 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	-0.87 Å²

Refinement step

Cycle: LAST / Resolution: 2→90.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7575	0	97	739	8411

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.021	7985
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.679	1.935	10912
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.118	5	931
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.007	23.724	392
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.916	15	1167
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.35	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	1080
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6324
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	3492
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	5136
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	614
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	0.209	0.2	78
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.232	0.2	30
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	1.018	1.5	4852
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.481	2	7641
X-RAY DIFFRACTION	r_scbond_it	2.508	3	3747
X-RAY DIFFRACTION	r_scangle_it	3.562	4.5	3271
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.055 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.407	302	-
R_work	0.297	5583	-
obs	-	-	96.46 %

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	1.7845	1.3189	-0.6554	2.5398	-0.0536	0.4396	0.0849	-0.1458	-0.1915	0.4135	-0.1904	-0.3644	0.1241	0.0763	0.1055	0.1286	-0.0101	-0.0526	0.0106	0.0681	0.0005	50.7313	16.0463	50.9154
2	0.7371	-0.0642	-0.1228	0.1655	0.0429	0.5506	0.0044	0.0217	-0.0051	0.0153	-0.0425	0.0189	-0.0122	-0.0398	0.038	0.0226	0.0006	-0.0066	0.0496	-0.0087	0.0502	51.0874	37.443	35.192
3	4.2895	-3.648	-1.7983	3.3475	1.9806	1.5845	0.0173	0.0511	0.2728	-0.0855	0.0935	-0.2702	-0.193	-0.127	-0.1108	0.0721	0.0382	0.0003	0.0564	0.0044	0.0198	54.9271	42.0574	22.7653
4	3.3144	-0.1092	-0.2427	2.9002	1.7078	3.7108	0.0898	0.2197	0.1848	-0.2795	-0.0777	-0.2742	-0.4112	-0.0264	-0.0121	0.053	-0.0054	0.039	0.015	0.0175	0.0482	57.2317	51.5483	28.3339
5	1.7895	-1.7804	-0.3789	4.0996	2.9317	2.8835	-0.0874	-0.0267	-0.0209	-0.0142	0.2287	-0.1051	0.036	0.2613	-0.1413	0.0291	-0.0056	-0.0045	0.0522	-0.0282	0.0372	64.0888	31.8665	31.4211
6	0.9343	0.0581	0.0517	0.8811	-0.1471	0.5224	-0.068	-0.0324	0.0084	-0.0409	0.0653	0.0285	0.0709	-0.0314	0.0027	0.0373	-0.0001	-0.0212	0.0373	-0.0115	0.0399	47.9164	21.0022	19.1237
7	2.7373	-5.5537	-0.9979	12.937	0.9978	0.9953	0.0357	0.3746	-0.0517	0.0393	-0.2257	0.2622	0.4	-0.4339	0.19	0.0096	-0.1021	-0.0383	0.0787	-0.0024	0.0163	39.4193	13.8393	11.3033
8	1.7572	-0.342	0.2763	1.2713	-0.9518	3.1414	-0.1168	0.2595	-0.1472	-0.3801	0.0375	-0.09	0.4004	-0.2982	0.0793	0.0798	-0.0536	-0.0362	0.0808	-0.0465	-0.036	47.2615	17.7204	5.8997
9	1.1802	1.1246	-0.1393	1.0717	-0.1316	0.0261	0.0333	-0.0273	-0.1266	0.0442	-0.2214	0.1156	0.145	-0.0986	0.1881	0.0568	-0.0012	0.0017	0.0083	0.0231	0.0343	45.5065	13.8243	39.8439
10	0.3489	0.6117	0.2676	2.1221	0.3915	0.7465	0.0898	-0.0776	-0.0247	0.1435	-0.1207	0.1762	0.0924	0.0162	0.0309	0.0427	-0.0535	0.0293	0.0202	-0.0047	0.0472	42.0624	19.5845	44.4381
11	0.3555	0.1715	-0.0126	0.7135	-0.2988	0.3488	0.0651	-0.0146	-0.0334	-0.1234	-0.0444	-0.0121	0.0794	-0.0001	-0.0207	0.069	0.0168	-0.0019	0.0182	-0.0054	0.0174	70.9977	-4.3244	18.7797
12	3.604	-2.2877	2.8318	2.0727	-1.3241	2.5863	0.1675	-0.2854	-0.4648	0.0594	0.0656	0.1715	0.165	-0.3641	-0.233	0.0249	-0.0214	0.0034	0.1205	0.0277	0.0191	62.0399	-13.7614	36.7212
13	8.2359	3.0636	0.0841	2.1781	-1.7064	8.5786	0.0362	-0.0473	-0.3814	0.1204	-0.0622	0.0893	0.3967	-0.336	0.026	0.103	-0.1059	-0.0106	-0.0347	0.0082	0.0259	55.9447	-21.9104	28.6032
14	0.7442	0.7065	0.9024	0.8115	1.3929	3.1363	0.1584	0.0479	-0.1743	0.0106	0.0566	-0.2487	0.2891	0.2509	-0.215	0.0708	0.0354	-0.0383	0.0249	-0.0018	0.0563	77.4648	-14.5448	31.9189
15	0.8902	0.2814	0.2242	0.9379	0.2416	0.4846	0.072	-0.003	0.0706	-0.0546	-0.0988	0.0145	-0.0087	-0.0079	0.0268	0.0312	-0.0102	0.0035	0.0449	0.0004	0.0377	76.7211	3.8556	40.5122
16	25.6657	4.4068	2.0069	3.9719	2.9641	2.291	0.0356	-0.5869	0.6761	-0.0218	-0.0297	0.2911	-0.553	0.2161	-0.0059	0.0323	-0.0793	0.0114	-0.0105	-0.0018	0.0398	83.031	15.1754	47.6277
17	4.4494	-0.9907	3.5716	2.362	-2.9937	9.2831	-0.0025	-0.4501	0.4201	0.4703	-0.1761	-0.0555	-0.6304	-0.2435	0.1787	0.0821	-0.0704	0.0211	0.0194	-0.0926	0.0329	75.0591	10.1212	55.6943
18	0.2212	-0.0233	0.0488	0.1986	-0.2387	1.2525	0.0397	-0.018	0.0245	-0.0361	-0.0756	-0.0133	0.036	0.1511	0.0359	0.0188	-0.0082	0.0213	0.0248	0.0058	0.0512	82.7226	5.0112	29.634
19	0.3894	0.5436	0.2063	1.1379	-0.1019	0.5101	0.0642	-0.0011	0.0245	-0.0869	-0.0872	-0.0022	0.0075	0.0718	0.023	0.0457	0.0179	0.019	0.0344	0.008	0.0338	76.1507	7.9706	15.5774
20	19.6835	-13.6858	7.3995	13.4566	-0.2517	8.8567	1.1334	1.5526	-0.56	-0.9641	-1.4786	-0.0058	0.2121	0.4772	0.3452	0.1829	0.1001	0.0267	0.0527	-0.0056	0.0055	66.7119	16.8883	-0.2237
21	10.9046	1.3753	2.1278	0.6827	0.567	6.6511	-0.3441	-0.7927	0.4239	0.3071	0.0947	-0.1172	-0.2104	-0.0661	0.2494	-0.0074	-0.0013	-0.0767	0.0663	-0.0615	0.0372	88.4362	40.0746	29.5162
22	1.0993	-0.1056	0.2349	0.2909	-0.2667	1.1342	-0.1182	-0.0216	0.1436	-0.112	-0.054	-0.0106	-0.1348	0.0051	0.1722	0.0402	-0.0057	-0.0101	-0.0093	0.0254	0.0434	71.1338	40.4013	9.0625
23	0.175	0.0472	-0.0177	0.6896	-0.3464	0.6288	-0.0332	-0.0401	-0.0215	-0.1278	0.0194	0.013	0.0065	0.0168	0.0138	0.0594	0.0082	-0.0138	0.0394	0.0059	0.0289	63.7804	32.8636	3.2437
24	2.3919	1.9463	-0.045	3.6417	-0.3239	1.5146	-0.0493	0.0216	0.1636	-0.2595	0.0851	0.2561	-0.0507	-0.1901	-0.0357	0.0297	0.0112	-0.0552	0.0335	0.0355	0.0131	52.7949	36.0231	1.7293
25	2.6339	-0.732	-0.2692	1.3188	-0.4303	0.9394	0.0684	0.0602	-0.1395	0.0357	-0.1539	0.0301	-0.077	0.1078	0.0855	0.0209	-0.0094	0.0046	0.0089	0.0352	0.0398	79.5687	40.6734	-10.4635
26	2.9043	-0.3671	0.0694	0.3298	0.2581	0.7076	-0.001	-0.0397	0.0198	0.0133	-0.0602	-0.0422	0.0268	0.0847	0.0612	0.0541	-0.0092	0.0424	0.0201	0.0526	0.0222	81.4145	38.5657	-9.8232
27	10.0673	3.2924	-0.2317	1.117	0.3922	5.4408	-0.1644	0.553	-0.5068	-0.1586	0.1956	-0.9653	0.355	0.2151	-0.0311	-0.0518	0.1115	0.0822	0.0173	-0.0344	0.0714	89.331	33.8973	-20.7185
28	2.0832	1.8905	1.6905	2.5961	1.7886	4.9307	-0.0287	0.2561	0.0445	-0.1593	0.0768	-0.1501	-0.2656	0.2596	-0.0481	0.0138	0.0237	0.0105	0.0251	0.0502	0.0338	82.6207	44.7817	-19.7837
29	0.9495	0.1661	-0.3722	0.1521	-0.415	2.0453	-0.1094	0.0311	0.0791	0.0066	-0.0098	0.0096	0.019	0.3198	0.1191	-0.0376	-0.0243	-0.0191	0.0925	0.0353	0.0891	87.5871	37.1151	12.4864
30	1.8084	-0.3125	0.7644	0.4461	0.4831	1.2884	-0.032	-0.0205	-0.0027	0.0489	-0.0187	-0.0968	-0.1395	0.2016	0.0506	-0.0302	-0.0112	0.0048	0.0625	0.0243	0.0601	83.1719	34.3016	16.9634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	206 - 236	7 - 37
2	X-RAY DIFFRACTION	2	A	A	237 - 295	38 - 96
3	X-RAY DIFFRACTION	3	A	A	296 - 308	97 - 109
4	X-RAY DIFFRACTION	4	A	A	309 - 326	110 - 127
5	X-RAY DIFFRACTION	5	A	A	327 - 342	128 - 143
6	X-RAY DIFFRACTION	6	A	A	343 - 402	144 - 203
7	X-RAY DIFFRACTION	7	A	A	403 - 415	204 - 216
8	X-RAY DIFFRACTION	8	A	A	416 - 441	217 - 242
9	X-RAY DIFFRACTION	9	A	A	442 - 461	243 - 262
10	X-RAY DIFFRACTION	10	A	A	462 - 518	263 - 319
11	X-RAY DIFFRACTION	11	B	B	205 - 294	6 - 95
12	X-RAY DIFFRACTION	12	B	B	295 - 309	96 - 110
13	X-RAY DIFFRACTION	13	B	B	314 - 326	115 - 127
14	X-RAY DIFFRACTION	14	B	B	327 - 346	128 - 147
15	X-RAY DIFFRACTION	15	B	B	347 - 403	148 - 204
16	X-RAY DIFFRACTION	16	B	B	404 - 412	205 - 213
17	X-RAY DIFFRACTION	17	B	B	413 - 429	214 - 230
18	X-RAY DIFFRACTION	18	B	B	430 - 461	231 - 262
19	X-RAY DIFFRACTION	19	B	B	462 - 517	263 - 318
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