PDB-7bfd: Circular permutant of ribosomal protein S6, P54-55 truncated, Y4A...

ID or keywords:

Entry

Database: PDB / ID: 7bfd

Title

Circular permutant of ribosomal protein S6, P54-55 truncated, Y4A mutant.

Components

30S ribosomal protein S6,30S ribosomal protein S6

Keywords

RIBOSOMAL PROTEIN / Circular permutant / native stacking / / designed amyloid fibril

Function / homology

Function and homology information

small ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.57 Å

Authors

Wang, H. / Logan, D.T. / Oliveberg, M.

Citation

Journal: To Be Published
Title: Circular permutant of ribosomal protein S6
Authors: Wang, H. / Logan, D.T. / Oliveberg, M.

History

Deposition	Jan 2, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7bfd_validation.pdf.gz	523 KB	Display	wwPDB validaton report
Full document	7bfd_full_validation.pdf.gz	549.7 KB	Display
Data in XML	7bfd_validation.xml.gz	35.3 KB	Display
Data in CIF	7bfd_validation.cif.gz	50.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/7bfd ftp://data.pdbj.org/pub/pdb/validation_reports/bf/7bfd	HTTPS FTP

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Related structure data

Related structure data	7bfcC 7bfeC 7bffC 7bfgC 1risS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#121 - Jan 2010 70S Ribosomes similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #10 - Oct 2000 Ribosome similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1)

Deposited unit

A: 30S ribosomal protein S6,30S ribosomal protein S6

B: 30S ribosomal protein S6,30S ribosomal protein S6

J: 30S ribosomal protein S6,30S ribosomal protein S6

K: 30S ribosomal protein S6,30S ribosomal protein S6

L: 30S ribosomal protein S6,30S ribosomal protein S6

C: 30S ribosomal protein S6,30S ribosomal protein S6

D: 30S ribosomal protein S6,30S ribosomal protein S6

E: 30S ribosomal protein S6,30S ribosomal protein S6

F: 30S ribosomal protein S6,30S ribosomal protein S6

G: 30S ribosomal protein S6,30S ribosomal protein S6

H: 30S ribosomal protein S6,30S ribosomal protein S6

I: 30S ribosomal protein S6,30S ribosomal protein S6

120 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: microscopy

Unit cell

Length a, b, c (Å)	61.041, 75.063, 223.592
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	-38 - 45
2	1	1	B	-38 - 45
1	2	2	A	-38 - 45
2	2	2	J	-38 - 45
1	3	3	A	-38 - 45
2	3	3	K	-38 - 45
1	4	4	A	-38 - 45
2	4	4	L	-38 - 45
1	5	5	A	-38 - 45
2	5	5	C	-38 - 45
1	6	6	A	-38 - 45
2	6	6	D	-38 - 45
1	7	7	A	-38 - 45
2	7	7	E	-38 - 45
1	8	8	A	-38 - 45
2	8	8	F	-38 - 45
1	9	9	A	-38 - 45
2	9	9	G	-38 - 45
1	10	10	A	-38 - 45
2	10	10	H	-38 - 45
1	11	11	A	-38 - 45
2	11	11	I	-38 - 45
1	12	12	B	-38 - 45
2	12	12	J	-38 - 45
1	13	13	B	-38 - 45
2	13	13	K	-38 - 45
1	14	14	B	-38 - 45
2	14	14	L	-38 - 45
1	15	15	B	-38 - 45
2	15	15	C	-38 - 45
1	16	16	B	-38 - 45
2	16	16	D	-38 - 45
1	17	17	B	-38 - 45
2	17	17	E	-38 - 45
1	18	18	B	-38 - 45
2	18	18	F	-38 - 45
1	19	19	B	-38 - 45
2	19	19	G	-38 - 45
1	20	20	B	-38 - 45
2	20	20	H	-38 - 45
1	21	21	B	-38 - 45
2	21	21	I	-38 - 45
1	22	22	J	-38 - 45
2	22	22	K	-38 - 45
1	23	23	J	-38 - 45
2	23	23	L	-38 - 45
1	24	24	J	-38 - 45
2	24	24	C	-38 - 45
1	25	25	J	-38 - 45
2	25	25	D	-38 - 45
1	26	26	J	-38 - 45
2	26	26	E	-38 - 45
1	27	27	J	-38 - 45
2	27	27	F	-38 - 45
1	28	28	J	-38 - 45
2	28	28	G	-38 - 45
1	29	29	J	-38 - 45
2	29	29	H	-38 - 45
1	30	30	J	-38 - 45
2	30	30	I	-38 - 45
1	31	31	K	-38 - 45
2	31	31	L	-38 - 45
1	32	32	K	-38 - 45
2	32	32	C	-38 - 45
1	33	33	K	-38 - 45
2	33	33	D	-38 - 45
1	34	34	K	-38 - 45
2	34	34	E	-38 - 45
1	35	35	K	-38 - 45
2	35	35	F	-38 - 45
1	36	36	K	-38 - 45
2	36	36	G	-38 - 45
1	37	37	K	-38 - 45
2	37	37	H	-38 - 45
1	38	38	K	-38 - 45
2	38	38	I	-38 - 45
1	39	39	L	-38 - 45
2	39	39	C	-38 - 45
1	40	40	L	-38 - 45
2	40	40	D	-38 - 45
1	41	41	L	-38 - 45
2	41	41	E	-38 - 45
1	42	42	L	-38 - 45
2	42	42	F	-38 - 45
1	43	43	L	-38 - 45
2	43	43	G	-38 - 45
1	44	44	L	-38 - 45
2	44	44	H	-38 - 45
1	45	45	L	-38 - 45
2	45	45	I	-38 - 45
1	46	46	C	-38 - 45
2	46	46	D	-38 - 45
1	47	47	C	-38 - 45
2	47	47	E	-38 - 45
1	48	48	C	-38 - 45
2	48	48	F	-38 - 45
1	49	49	C	-38 - 45
2	49	49	G	-38 - 45
1	50	50	C	-38 - 45
2	50	50	H	-38 - 45
1	51	51	C	-38 - 45
2	51	51	I	-38 - 45
1	52	52	D	-38 - 45
2	52	52	E	-38 - 45
1	53	53	D	-38 - 45
2	53	53	F	-38 - 45
1	54	54	D	-38 - 45
2	54	54	G	-38 - 45
1	55	55	D	-38 - 45
2	55	55	H	-38 - 45
1	56	56	D	-38 - 45
2	56	56	I	-38 - 45
1	57	57	E	-38 - 45
2	57	57	F	-38 - 45
1	58	58	E	-38 - 45
2	58	58	G	-38 - 45
1	59	59	E	-38 - 45
2	59	59	H	-38 - 45
1	60	60	E	-38 - 45
2	60	60	I	-38 - 45
1	61	61	F	-38 - 45
2	61	61	G	-38 - 45
1	62	62	F	-38 - 45
2	62	62	H	-38 - 45
1	63	63	F	-38 - 45
2	63	63	I	-38 - 45
1	64	64	G	-38 - 45
2	64	64	H	-38 - 45
1	65	65	G	-38 - 45
2	65	65	I	-38 - 45
1	66	66	H	-38 - 45
2	66	66	I	-38 - 45

NCS ensembles :

#1: Protein	30S ribosomal protein S6,30S ribosomal protein S6 / TS9 / TS9 Mass: 10039.454 Da / Num. of mol.: 12 / Mutation: Y4A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rpsF, TTHA0245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLP8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate dibasic 20% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

MAX IV

/ Beamline: BioMAX / Wavelength: 0.75142 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.75142 Å / Relative weight: 1

Reflection

Resolution: 2.57→47.9 Å / Num. obs: 33539 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC_1/2: 0.997 / R_merge(I) obs: 0.174 / R_pim(I) all: 0.074 / R_rim(I) all: 0.189 / Net I/σ(I): 8.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.57-2.66	5.4	1.31	17082	3160	0.69	0.619	1.454	1.1	97.6
9.95-47.36	5.6	0.044	3792	683	0.999	0.019	0.048	30.6	99.1

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Processing

Software

Name	Version	Classification
Aimless	0.7.2	data scaling
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ris

1ris

Resolution: 2.57→47.4 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.916 / SU B: 48.135 / SU ML: 0.426 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2972	1622	4.8 %	RANDOM
R_work	0.2567	-	-	-
obs	0.2587	31839	99.44 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 160.84 Å² / B_iso mean: 70.507 Å² / B_iso min: 30.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.93 Å²	0 Å²	0 Å²
2-	-	3.33 Å²	0 Å²
3-	-	-	-7.27 Å²

Refinement step

Cycle: final / Resolution: 2.57→47.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8208	0	0	23	8231
B_iso mean	-	-	-	48.52	-
Num. residues	-	-	-	-	1008

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	8304
X-RAY DIFFRACTION	r_angle_refined_deg	1.773	1.641	11232
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.618	5	996
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.366	21.458	576
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.666	15	1536
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.247	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	1032
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6468

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	2571	0.11
1	2	B	2571	0.11
2	1	A	2633	0.08
2	2	J	2633	0.08
3	1	A	2422	0.15
3	2	K	2422	0.15
4	1	A	2590	0.11
4	2	L	2590	0.11
5	1	A	2599	0.11
5	2	C	2599	0.11
6	1	A	2629	0.08
6	2	D	2629	0.08
7	1	A	2570	0.11
7	2	E	2570	0.11
8	1	A	2606	0.11
8	2	F	2606	0.11
9	1	A	2620	0.08
9	2	G	2620	0.08
10	1	A	2548	0.12
10	2	H	2548	0.12
11	1	A	2607	0.11
11	2	I	2607	0.11
12	1	B	2538	0.12
12	2	J	2538	0.12
13	1	B	2450	0.13
13	2	K	2450	0.13
14	1	B	2538	0.11
14	2	L	2538	0.11
15	1	B	2587	0.12
15	2	C	2587	0.12
16	1	B	2559	0.11
16	2	D	2559	0.11
17	1	B	2604	0.09
17	2	E	2604	0.09
18	1	B	2587	0.12
18	2	F	2587	0.12
19	1	B	2541	0.12
19	2	G	2541	0.12
20	1	B	2537	0.1
20	2	H	2537	0.1
21	1	B	2548	0.13
21	2	I	2548	0.13
22	1	J	2380	0.16
22	2	K	2380	0.16
23	1	J	2540	0.12
23	2	L	2540	0.12
24	1	J	2541	0.11
24	2	C	2541	0.11
25	1	J	2589	0.09
25	2	D	2589	0.09
26	1	J	2512	0.12
26	2	E	2512	0.12
27	1	J	2543	0.11
27	2	F	2543	0.11
28	1	J	2576	0.09
28	2	G	2576	0.09
29	1	J	2490	0.12
29	2	H	2490	0.12
30	1	J	2557	0.11
30	2	I	2557	0.11
31	1	K	2394	0.16
31	2	L	2394	0.16
32	1	K	2429	0.15
32	2	C	2429	0.15
33	1	K	2460	0.15
33	2	D	2460	0.15
34	1	K	2479	0.13
34	2	E	2479	0.13
35	1	K	2420	0.15
35	2	F	2420	0.15
36	1	K	2397	0.16
36	2	G	2397	0.16
37	1	K	2435	0.13
37	2	H	2435	0.13
38	1	K	2412	0.15
38	2	I	2412	0.15
39	1	L	2608	0.09
39	2	C	2608	0.09
40	1	L	2544	0.11
40	2	D	2544	0.11
41	1	L	2530	0.11
41	2	E	2530	0.11
42	1	L	2601	0.09
42	2	F	2601	0.09
43	1	L	2538	0.11
43	2	G	2538	0.11
44	1	L	2508	0.12
44	2	H	2508	0.12
45	1	L	2619	0.09
45	2	I	2619	0.09
46	1	C	2598	0.11
46	2	D	2598	0.11
47	1	C	2574	0.1
47	2	E	2574	0.1
48	1	C	2710	0.06
48	2	F	2710	0.06
49	1	C	2571	0.11
49	2	G	2571	0.11
50	1	C	2506	0.12
50	2	H	2506	0.12
51	1	C	2638	0.09
51	2	I	2638	0.09
52	1	D	2587	0.11
52	2	E	2587	0.11
53	1	D	2602	0.11
53	2	F	2602	0.11
54	1	D	2607	0.08
54	2	G	2607	0.08
55	1	D	2483	0.12
55	2	H	2483	0.12
56	1	D	2570	0.11
56	2	I	2570	0.11
57	1	E	2579	0.1
57	2	F	2579	0.1
58	1	E	2548	0.12
58	2	G	2548	0.12
59	1	E	2532	0.09
59	2	H	2532	0.09
60	1	E	2555	0.11
60	2	I	2555	0.11
61	1	F	2590	0.11
61	2	G	2590	0.11
62	1	F	2515	0.11
62	2	H	2515	0.11
63	1	F	2646	0.08
63	2	I	2646	0.08
64	1	G	2506	0.12
64	2	H	2506	0.12
65	1	G	2551	0.12
65	2	I	2551	0.12
66	1	H	2536	0.12
66	2	I	2536	0.12

LS refinement shell

Resolution: 2.57→2.637 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.382	119	-
R_work	0.413	2210	-
all	-	2329	-
obs	-	-	95.84 %

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	4.1336	-0.6963	-0.4163	6.1431	1.1443	5.9741	-0.2346	-0.1773	-0.311	-0.0105	0.0492	0.2149	0.3094	-0.3707	0.1854	0.064	-0.0406	0.0418	0.0815	-0.0019	0.0451	-2.9494	2.8116	195.9405
2	3.585	-2.5815	0.6345	5.4822	-2.2611	5.4178	-0.0902	-0.0241	0.1183	-0.123	-0.199	-0.2204	-0.6454	0.4248	0.2893	0.3138	0.0329	0.0146	0.0663	0.0395	0.0285	5.7052	9.0189	215.0525
3	1.1538	0.501	-0.8748	7.9443	1.0361	5.2991	0.0409	0.2831	0.0458	0.2068	-0.0386	0.4421	0.0571	-0.551	-0.0023	0.0899	-0.0297	0.0216	0.1242	-0.0033	0.028	-4.133	9.9923	140.9466
4	4.7195	3.5136	-0.4741	8.1295	-1.3329	4.7884	-0.2545	0.0115	-0.0435	-0.4976	0.009	-0.4744	0.4242	0.0632	0.2455	0.266	-0.0261	0.0655	0.0222	-0.0057	0.0459	4.5722	1.9049	158.6618
5	4.6575	1.3562	1.4181	3.9491	-0.5249	6.5589	-0.0152	-0.0055	0.2121	-0.0278	-0.1822	-0.0628	0.018	-0.0434	0.1974	0.0938	-0.0336	0.0226	0.0236	-0.0037	0.021	3.1867	12.6211	177.4987
6	1.972	-2.0375	0.3927	8.5266	0.0525	5.3852	0.0496	-0.2078	-0.1478	-0.2229	-0.1055	0.5953	-0.0407	-0.3699	0.0559	0.1503	0.0473	-0.0563	0.0796	-0.0289	0.0583	-5.3037	7.2117	9.9982
7	6.418	-0.9627	0.1847	3.0042	0.3804	3.4907	-0.1308	0.085	0.3517	-0.1176	-0.1484	-0.353	-0.3355	0.2431	0.2792	0.1171	-0.0712	-0.0384	0.2695	0.0625	0.0833	1.4203	12.9176	84.6691
8	2.65	-1.702	-0.161	4.645	0.1116	4.4883	0.1031	0.0358	-0.2076	-0.191	-0.1414	0.36	0.0159	-0.1882	0.0383	0.071	0.0043	-0.0434	0.1083	-0.0163	0.0432	-6.8666	5.6318	103.4395
9	1.3138	0.2231	-0.6216	7.2417	0.6325	4.7777	0.0278	-0.2057	0.0539	-0.0811	-0.0081	-0.1766	0.1323	0.1119	-0.0197	0.0273	0.006	-0.0207	0.0807	0.0035	0.0524	5.2491	7.5083	121.3743
10	1.7222	0.7183	-0.6291	8.5438	-1.8361	3.9159	0.0681	-0.1797	0.0026	-0.1465	-0.13	-0.4003	0.3049	0.3452	0.0619	0.1983	-0.0061	-0.0021	0.2249	-0.0036	0.0204	5.6198	4.1312	28.8675
11	8.1472	1.1755	2.4717	5.2386	-0.0984	5.859	-0.5242	-0.2271	0.3591	0.068	0.1018	0.1885	-0.4799	-0.3861	0.4225	0.2337	0.0321	-0.0414	0.2029	-0.0591	0.0468	-2.4053	13.4728	46.3099
12	7.7615	0.382	-0.2054	4.8529	0.3345	4.0248	0.3533	0.4515	-0.6459	-0.4829	-0.3559	0.329	0.3856	-0.4038	0.0026	0.1804	0.0294	-0.0652	0.3899	-0.0241	0.0862	-2.4338	4.1923	65.5594

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-38 - 45
2	X-RAY DIFFRACTION	2	B	-38 - 45
3	X-RAY DIFFRACTION	3	J	-38 - 45
4	X-RAY DIFFRACTION	4	K	-38 - 45
5	X-RAY DIFFRACTION	5	L	-38 - 45
6	X-RAY DIFFRACTION	6	C	-38 - 45
7	X-RAY DIFFRACTION	7	D	-38 - 45
8	X-RAY DIFFRACTION	8	E	-38 - 45
9	X-RAY DIFFRACTION	9	F	-38 - 45
10	X-RAY DIFFRACTION	10	G	-38 - 45
11	X-RAY DIFFRACTION	11	H	-38 - 45
12	X-RAY DIFFRACTION	12	I	-38 - 45

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