PDB-4a75: The Lin28b Cold shock domain in complex with hexathymidine.

ID or keywords:

Entry

Database: PDB / ID: 4a75

Title

The Lin28b Cold shock domain in complex with hexathymidine.

Components

5'-D(*TP*TP*TP*TP*TP*TP)-3'
LIN28 COLD SHOCK DOMAIN

Keywords

CHAPERONE/DNA / CHAPERONE-DNA COMPLEX / CHAPERONE / DNA/RNA-BINDING PROTEIN

Function / homology

Function and homology information

regulatory ncRNA-mediated gene silencing / nucleic acid binding / nucleolus / zinc ion binding
Similarity search - Function

Biological species

XENOPUS TROPICALIS
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 1.75 Å

Authors

Mayr, F. / Schuetz, A. / Doege, N. / Heinemann, U.

Citation

Journal: Nucleic Acids Res. / Year: 2012
Title: The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna.
Authors: Mayr, F. / Schutz, A. / Doge, N. / Heinemann, U.

History

Deposition	Nov 11, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.2	Oct 9, 2019	Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_entity_src_syn / reflns / reflns_shell Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs ..._pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_sigmaI
Revision 1.3	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4a75.cif.gz	169 KB	Display	PDBx/mmCIF format
PDB format	pdb4a75.ent.gz	135.5 KB	Display	PDB format
PDBx/mmJSON format	4a75.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/a7/4a75 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a75	HTTPS FTP

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Related structure data

Related structure data	3uljC 4a4iC 4a76C 4alpC C: citing same article (ref.)
Similar structure data	5m6m-d 1jer-d 3ahs-2 2uwq-d 2la8-d 3imd-1 2kg0-d 6r0q-1 2mp1-d 4xjj-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

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	#32 - Aug 2002 Chaperones similarity (1) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: LIN28 COLD SHOCK DOMAIN

B: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

C: LIN28 COLD SHOCK DOMAIN

D: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

E: LIN28 COLD SHOCK DOMAIN

F: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

G: LIN28 COLD SHOCK DOMAIN

H: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

hetero molecules

47 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: LIN28 COLD SHOCK DOMAIN

B: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

hetero molecules

defined by author&software
11.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: LIN28 COLD SHOCK DOMAIN

D: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

defined by author&software
11.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: LIN28 COLD SHOCK DOMAIN

F: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

hetero molecules

defined by author&software
11.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: LIN28 COLD SHOCK DOMAIN

H: 5'-D(*TP*TP*TP*TP*TP*TP)-3'

defined by author&software
11.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.799, 81.822, 99.819
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	LIN28 COLD SHOCK DOMAIN Mass: 9942.231 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4F6I0
#2: DNA chain	5'-D(TPTPTPTPTPTP)-3' / HEXATHYMIDINE Mass: 1780.199 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.47 % / Description: NONE
Crystal grow	Temperature: 277 K / Method: vapor diffusion Details: 0.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 ...Details: 0.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 M sodium thiocyanate as reservoir buffer

Crystal

Density Matthews: 2.26 Å³/Da / Density % sol: 45.47 % / Description: NONE

Crystal grow

Temperature: 277 K / Method: vapor diffusion
Details: 0.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: BL14-1 / Type: BESSY / Wavelength: 0.98141
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98141 Å / Relative weight: 1
Reflection	Resolution: 1.75→32.91 Å / Num. obs: 39188 / % possible obs: 89.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / R_merge(I) obs: 0.06 / R_rim(I) all: 0.078 / Net I/σ(I): 13.2
Reflection shell	Resolution: 1.75→1.85 Å / Mean I/σ(I) obs: 3.3 / R_rim(I) all: 0.39 / % possible all: 87.8

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Processing

Software

Name: REFMAC / Version: 5.5.0109 / Classification: refinement

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.75→32.91 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.942 / SU B: 3.836 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19801	2110	5 %	RANDOM
R_work	0.17105	-	-	-
obs	0.17239	40088	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 14.67 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.28 Å²	0 Å²	0 Å²
2-	-	0.67 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→32.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2734	400	6	506	3646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3302
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2278
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	2.114	4515
X-RAY DIFFRACTION	r_angle_other_deg	0.983	3	5539
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.292	5	368
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.172	23.125	128
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.963	15	495
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.295	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	458
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	3435
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	669
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	1.731	5	1773
X-RAY DIFFRACTION	r_mcbond_other	0.476	5	740
X-RAY DIFFRACTION	r_mcangle_it	2.71	7	2842
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.59	9	1529
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.778	11	1666
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.748→1.793 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	145	-
R_work	0.222	2761	-
obs	-	-	100 %

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	4.1393	0.5199	-1.0469	7.1952	1.4839	4.1132	0.0412	-0.4585	-0.0241	0.438	-0.028	-0.3969	0.1101	0.2832	-0.0132	0.1049	-0.0022	0.0124	0.0924	0.0072	0.0791	16.7233	-3.8768	-0.2401
2	0.8987	0.79	-1.799	1.8451	-0.5789	6.1538	-0.026	0.0704	-0.0058	-0.0229	-0.0062	-0.1026	0.0287	0.0672	0.0322	0.0146	0.0017	-0.0058	0.058	0.0038	0.0666	5.6102	-8.94	-19.7828
3	2.0727	-0.2172	-1.0449	1.1064	-0.0849	2.1411	0.0129	-0.1168	-0.0438	0.1382	-0.002	0.0832	-0.016	-0.0324	-0.0109	0.0474	-0.0111	-0.0167	0.0317	-0.0105	0.0534	5.6526	-8.4854	-10.9256
4	9.6337	1.4031	-4.6777	2.1968	-0.206	6.2417	-0.0257	0.259	-0.2099	-0.1271	0.0146	0.0486	0.165	-0.0314	0.0111	0.1053	-0.0051	-0.0182	0.0358	-0.0123	0.0729	9.286	-16.2911	-21.3619
5	1.9057	-0.8243	-0.0192	3.8437	1.0208	1.2453	0.0058	0.0319	0.1184	-0.0243	-0.0082	-0.0744	-0.0716	0.0115	0.0023	0.0567	-0.0034	0.0002	0.0784	0.0033	0.045	10.8871	-6.2152	-9.745
6	2.3059	1.0957	-1.195	2.5409	0.3802	7.9529	0.1123	0.0811	-0.1261	-0.1984	0.03	0.1286	0.4072	-0.047	-0.1423	0.1123	0.0001	-0.0074	0.0761	-0.01	0.1217	9.9179	-20.7951	-16.2057
7	7.2758	6.2831	1.1891	7.2562	1.6748	3.0753	0.2324	-0.3158	0.0147	0.3533	-0.2473	0.2957	0.1531	-0.2854	0.0149	0.1052	0.0387	-0.0087	0.0869	0.0162	0.0899	28.5784	-13.3005	-4.4528
8	1.5666	-0.4522	0.3196	1.1968	-0.1181	2.7884	0.0253	-0.0599	-0.0919	0.022	-0.0173	-0.0157	0.1237	0.0631	-0.0079	0.0611	-0.0157	-0.0016	0.0521	-0.0171	0.093	32.86	-10.0333	-9.7578
9	2.8751	-0.1431	2.8289	3.7756	-2.2519	8.0213	-0.0697	0.1137	0.1815	0.0132	0.037	0.0126	-0.2428	-0.0132	0.0327	0.0665	0.0028	0.0163	0.0309	-0.0246	0.0745	30.9859	-0.5925	-11.0497
10	2.9143	0.0138	-0.1885	3.9828	0.1463	2.7273	-0.0189	0.1707	-0.2344	-0.169	0.0247	-0.1239	0.2051	0.1106	-0.0057	0.0416	-0.0007	-0.0107	0.107	0.0152	0.0433	27.1579	-9.8148	-8.7538
11	3.0292	-3.0317	-2.7834	3.3547	2.1174	4.3535	0.2188	0.0974	0.1954	-0.2442	-0.0718	-0.1963	-0.2413	0.0382	-0.147	0.0602	-0.029	-0.0272	0.0868	-0.0059	0.0898	33.9683	6.9693	4.5287
12	1.9773	-1.9047	2.5113	3.1444	-6.2253	16.2738	-0.0009	-0.1755	-0.1976	0.1166	0.0326	0.1764	0.0035	-0.2577	-0.0317	0.1099	-0.057	0.0138	0.1314	-0.0209	0.0958	33.2196	7.118	23.5151
13	2.2633	0.1507	0.9266	1.0763	-0.1223	1.6026	0.0222	0.1399	0.0269	-0.1767	-0.0094	0.1171	0.0529	-0.089	-0.0127	0.0662	0.0075	0.0145	0.0459	-0.0101	0.072	30.9274	6.9306	6.9155
14	4.097	-0.3955	0.6614	3.4129	-0.6772	7.1423	0.0828	-0.2801	0.4357	0.1212	-0.0703	-0.0009	-0.2666	0.1916	-0.0125	0.1107	0.0091	0.0022	0.0432	-0.0206	0.0859	37.7835	15.7012	17.4714
15	1.9584	-0.3811	-0.7615	2.9304	1.1467	1.6924	-0.0117	-0.0346	-0.106	0.0155	0.0217	-0.1245	0.0938	0.0505	-0.0101	0.0509	-0.0044	-0.0171	0.0846	0.0041	0.0452	34.6818	5.1135	6.336
16	1.1474	-0.0894	0.2572	2.5478	-0.339	2.0863	0.0241	-0.0885	0.1524	0.076	-0.02	0.1035	-0.2045	-0.1042	-0.0041	0.0559	-0.0066	-0.0064	0.0787	0.001	0.0774	37.6151	16.1862	10.102
17	2.7844	-0.4882	-0.5114	3.2813	0.8675	3.4359	0.0896	0.0171	-0.0663	-0.1539	0.0049	0.1472	0.0205	-0.1233	-0.0945	0.0645	-0.0557	0.0304	0.0652	-0.0154	0.0948	5.5195	9.8119	5.9178
18	1.5918	0.2325	-0.456	1.4446	-0.7397	3.8883	-0.0187	0.0445	-0.0095	-0.0817	0.0143	0.0009	0.0069	-0.0122	0.0045	0.027	0.0177	-0.006	0.0298	-0.0187	0.0651	5.4084	7.3521	5.5844
19	5.5662	-4.2983	-0.036	10.5084	-0.2027	1.8708	-0.0655	-0.0867	-0.0766	0.0406	0.0451	0.2624	-0.0519	-0.0607	0.0204	0.0608	-0.0248	0.014	0.0891	0.0104	0.0147	3.9563	8.1596	2.5463
20	1.83	-0.2291	-0.3248	3.9435	-0.2538	1.1819	-0.0135	-0.1406	0.0767	0.2876	0.0319	-0.1208	-0.0349	0.0951	-0.0184	0.0536	0.0033	0.0032	0.0974	0.0123	0.042	1.6438	6.5637	5.4769

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 31
2	X-RAY DIFFRACTION	2	A	32 - 45
3	X-RAY DIFFRACTION	3	A	46 - 73
4	X-RAY DIFFRACTION	4	A	74 - 85
5	X-RAY DIFFRACTION	5	A	86 - 103
6	X-RAY DIFFRACTION	6	A	104 - 113
7	X-RAY DIFFRACTION	7	C	28 - 38
8	X-RAY DIFFRACTION	8	C	39 - 74
9	X-RAY DIFFRACTION	9	C	75 - 87
10	X-RAY DIFFRACTION	10	C	88 - 113
11	X-RAY DIFFRACTION	11	E	27 - 39
12	X-RAY DIFFRACTION	12	E	40 - 44
13	X-RAY DIFFRACTION	13	E	45 - 72
14	X-RAY DIFFRACTION	14	E	73 - 82
15	X-RAY DIFFRACTION	15	E	83 - 98
16	X-RAY DIFFRACTION	16	E	99 - 113
17	X-RAY DIFFRACTION	17	G	27 - 43
18	X-RAY DIFFRACTION	18	G	44 - 81
19	X-RAY DIFFRACTION	19	G	82 - 92
20	X-RAY DIFFRACTION	20	G	93 - 113

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