PDB-2bx9: Crystal structure of B.subtilis Anti-TRAP protein, an antagonist ...

ID or keywords:

Entry

Database: PDB / ID: 2bx9

Title

Crystal structure of B.subtilis Anti-TRAP protein, an antagonist of TRAP-RNA interactions

Components

TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

Keywords

TRANSCRIPTION REGULATION / ANTI-TRAP

Function / homology

Function and homology information

identical protein binding / cytoplasm
Similarity search - Function

Biological species

BACILLUS SUBTILIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.8 Å

Authors

Shevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal Structure of Bacillus Subtilis Anti-Trap Protein, an Antagonist of Trap/RNA Interaction.
Authors: Shevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.

History

Deposition	Jul 26, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 30, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2bx9_validation.pdf.gz	515.9 KB	Display	wwPDB validaton report
Full document	2bx9_full_validation.pdf.gz	535.7 KB	Display
Data in XML	2bx9_validation.xml.gz	26.5 KB	Display
Data in CIF	2bx9_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/2bx9 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/2bx9	HTTPS FTP

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Related structure data

Similar structure data	3lcz-1 5v7l-1 1hei-d 4ojq-d 4oks-d 4ok6-d 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

Deposited unit

A: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

B: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

C: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

D: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

E: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

F: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

G: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

H: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

I: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

J: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

K: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

L: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	51.552, 60.125, 60.348
Angle α, β, γ (deg.)	113.99, 101.37, 100.50
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

#1: Protein	TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN / ANTI-TRAP / AT Mass: 5655.565 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET17AT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: O31466
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.4 Å³/Da / Density % sol: 48 %
Crystal grow	pH: 6.5 Details: CONDITIONS: 21-23 % (W/V) POLY(ETHYLENE) GLYCOL 5000 MONMETHYL ETHER; 0.1 M SODIUM CACODYLATE PH 6.5; 50 MM MAGNESIUM ACETATE CRYOSOLUTION: 16 % GLYCEROL (V/V) WITH HIGHER CONCENTRATION OF POLY(ETHYLENE) GLYCOL

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Data collection

Diffraction

Mean temperature: 120 K

Diffraction source

Source:

SYNCHROTRON / Site:

SRS

/ Beamline: PX9.6 / Wavelength: 0.87, 1.28258

Detector

Type: ADSC CCD / Detector: CCD / Date: Jun 27, 2003

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.87	1
2	1.28258	1

Reflection

Resolution: 2.8→20 Å / Num. obs: 14370 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / R_merge(I) obs: 0.11 / Net I/σ(I): 5.7

Reflection shell

Resolution: 2.8→2.95 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.18 / Mean I/σ(I) obs: 2.4 / % possible all: 83

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
SHELXD		phasing
SHARP		phasing
REFMAC	5.2.0013	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.8→20 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.85 / SU B: 41.427 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.296	724	5 %	RANDOM
R_work	0.192	-	-	-
obs	0.197	13637	94.2 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 75.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.28 Å²	-0.07 Å²	0.48 Å²
2-	-	0.68 Å²	0.59 Å²
3-	-	-	-2.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4692	0	12	130	4834

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	4814
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.369	1.989	6487
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.14	5	624
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.53	26.433	171
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.124	15	855
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.978	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	768
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3448
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	2175
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	3244
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	193
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	0.259	0.2	77
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.062	0.2	8
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	1.043	2	3239
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.752	3	5055
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.893	6	1728
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.986	10	1432
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

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	204	tight positional	0.35	0.2
2	B	204	tight positional	0.39	0.2
3	C	204	tight positional	0.27	0.2
4	D	204	tight positional	0.64	0.2
5	E	204	tight positional	0.48	0.2
6	F	204	tight positional	0.75	0.2
7	G	204	tight positional	0.43	0.2
8	H	204	tight positional	0.79	0.2
9	I	204	tight positional	0.85	0.2
10	J	204	tight positional	0.4	0.2
11	K	204	tight positional	0.27	0.2
12	L	204	tight positional	0.27	0.2
1	A	58	medium positional	1.44	2
2	B	58	medium positional	1.13	2
3	C	58	medium positional	1.19	2
4	D	58	medium positional	1.67	2
5	E	58	medium positional	1.04	2
6	F	58	medium positional	1.84	2
7	G	58	medium positional	1.18	2
8	H	58	medium positional	1.86	2
9	I	58	medium positional	1.93	2
10	J	58	medium positional	1.54	2
11	K	58	medium positional	0.88	2
12	L	58	medium positional	1.31	2
1	A	102	loose positional	0.61	0.5
2	B	102	loose positional	0.74	0.5
3	C	102	loose positional	0.58	0.5
4	D	102	loose positional	0.69	0.5
5	E	102	loose positional	0.62	0.5
6	F	102	loose positional	1.08	0.5
7	G	102	loose positional	0.77	0.5
8	H	102	loose positional	0.99	0.5
9	I	102	loose positional	1.09	0.5
10	J	102	loose positional	0.74	0.5
11	K	102	loose positional	0.64	0.5
12	L	102	loose positional	0.6	0.5
1	A	204	tight thermal	0.48	2
2	B	204	tight thermal	0.39	2
3	C	204	tight thermal	0.42	2
4	D	204	tight thermal	0.6	2
5	E	204	tight thermal	0.52	2
6	F	204	tight thermal	0.57	2
7	G	204	tight thermal	0.57	2
8	H	204	tight thermal	0.49	2
9	I	204	tight thermal	0.64	2
10	J	204	tight thermal	0.42	2
11	K	204	tight thermal	0.61	2
12	L	204	tight thermal	0.44	2
1	A	58	medium thermal	3.19	10
2	B	58	medium thermal	2.45	10
3	C	58	medium thermal	2.19	10
4	D	58	medium thermal	3.92	10
5	E	58	medium thermal	2.73	10
6	F	58	medium thermal	2.62	10
7	G	58	medium thermal	3.77	10
8	H	58	medium thermal	2.7	10
9	I	58	medium thermal	3.54	10
10	J	58	medium thermal	2.07	10
11	K	58	medium thermal	3.89	10
12	L	58	medium thermal	1.88	10
1	A	102	loose thermal	4.12	10
2	B	102	loose thermal	3.86	10
3	C	102	loose thermal	3.35	10
4	D	102	loose thermal	2.83	10
5	E	102	loose thermal	3.89	10
6	F	102	loose thermal	3.65	10
7	G	102	loose thermal	3.73	10
8	H	102	loose thermal	3.08	10
9	I	102	loose thermal	3.64	10
10	J	102	loose thermal	2.95	10
11	K	102	loose thermal	3.39	10
12	L	102	loose thermal	3.44	10

LS refinement shell

Resolution: 2.8→2.95 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.404	99	-
R_work	0.253	1792	-
obs	-	-	87.02 %

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	9.1959	0.3117	3.2272	8.5286	-4.9976	16.578	0.0824	-0.4524	-0.2812	-0.2844	0.2591	-0.4	-0.0426	0.7134	-0.3416	-0.3109	-0.0468	0.0416	-0.0967	0.0021	-0.0326	22.3827	28.0229	29.5824
2	18.8892	3.1639	-11.1944	23.9297	-4.6376	17.0143	0.1867	0.3699	-0.6912	-1.8703	-0.806	-1.5815	0.6106	0.8641	0.6192	-0.0697	-0.0008	0.2011	0.0045	0.09	-0.0774	26.4516	36.6039	12.211
3	4.7968	-2.2956	-3.257	9.7665	4.0146	14.8156	-0.2509	0.4028	0.5335	0.324	0.1978	-0.9286	-0.0583	0.3518	0.0531	-0.3402	-0.0052	0.0588	-0.0082	0.0562	-0.0575	22.7634	21.8061	36.1214
4	21.0447	9.4112	11.6749	8.1196	1.8429	13.9522	0.9429	-0.5748	0.2509	0.7149	-0.1788	-1.6522	-1.7397	2.3538	-0.7641	0.1556	-0.3494	-0.058	0.4705	-0.2026	0.1783	27.4624	31.6817	51.6252
5	3.0786	0.3221	1.4201	11.9517	-0.8702	10.8228	-0.483	-0.2263	-0.1316	-0.016	0.3609	-1.0777	0.3375	0.6769	0.1221	-0.3171	0.0612	0.0699	-0.0491	-0.0115	-0.0942	22.2537	19.6798	27.2334
6	27.8518	-29.723	8.4991	32.8031	-3.6896	29.3194	0.8252	0.738	-2.3106	0.0422	0.6072	-0.7942	2.6077	2.9916	-1.4324	0.4367	0.2104	-0.18	0.2511	0.0037	0.6264	25.6354	0.894	28.9207
7	15.0498	-4.495	3.0479	8.624	-1.4301	5.4015	-0.1879	-0.069	0.2208	0.9452	0.1108	-0.2748	-0.4559	0.0145	0.0771	-0.2827	-0.0615	-0.0135	-0.2531	-0.0675	-0.3244	4.1159	28.7188	48.0294
8	10.7215	1.8496	0.2368	6.0684	-1.677	26.222	0.1308	-0.6287	-0.6377	0.8668	-0.6219	-0.8671	-1.1571	1.6775	0.4912	-0.1069	-0.0805	-0.1573	-0.1066	0.0455	-0.1033	18.8259	23.4084	59.9705
9	5.8351	0.7131	0.2769	17.7211	-5.7416	9.2779	0.2444	-0.2003	0.0591	0.4343	-0.3505	0.2868	0.1934	-0.1551	0.1061	-0.3681	0.0816	0.0239	-0.2817	-0.1048	-0.3269	-4.205	28.9086	44.7566
10	15.5349	-7.1831	-1.372	20.1126	7.1231	10.7918	-0.6971	-0.759	0.9829	0.7024	0.4048	-0.4687	-0.9129	0.133	0.2923	0.044	0.1594	-0.2036	-0.2389	-0.1351	0.0136	-7.813	48.111	45.6516
11	8.5972	4.9468	3.7916	11.1389	3.1853	11.8141	0.0907	-0.4956	0.1733	0.4687	-0.145	0.0802	-0.0595	-0.1645	0.0543	-0.3208	0.1013	0.0779	-0.2887	-0.0356	-0.3697	-0.6828	21.15	47.5956
12	27.4482	6.9394	-6.0964	10.0838	-6.2323	10.5897	0.4611	-1.1276	0.0962	0.8077	-0.0649	0.9292	0.3321	-1.2958	-0.3962	-0.1301	0.0056	0.0153	0.0347	0.0848	-0.0389	-17.7974	9.9248	47.3077
13	7.3656	1.7658	-0.3796	8.3468	4.8865	10.2698	0.0865	-0.1122	0.0965	-0.3609	-0.1862	-0.0805	-1.1121	-0.0717	0.0997	-0.146	-0.0318	-0.0157	-0.2508	0.1949	-0.2983	-4.5911	32.1406	19.1533
14	2.3963	-2.6682	2.5975	6.9882	-5.8693	32.4298	-0.5088	1.0821	-0.0342	-0.4759	0.6923	0.6141	0.0187	-3.1905	-0.1834	-0.1674	-0.1661	-0.0435	0.4141	0.0057	-0.1753	-8.8987	23.2559	2.1873
15	9.1953	-0.0541	-4.7073	4.0138	4.6987	12.099	0.0538	-0.2939	0.6903	-0.6015	0.1967	0.2506	-0.8115	0.1623	-0.2505	-0.014	-0.0132	-0.0401	-0.2475	0.0395	-0.2701	-1.464	37.8418	25.6535
16	17.5474	-6.8381	-8.1328	9.1749	2.5605	4.707	-0.0131	-0.599	1.442	-0.7995	-0.4055	1.2655	-0.6055	-0.6725	0.4186	0.0969	0.2219	-0.1768	0.0635	-0.2227	0.1851	-17.123	44.1567	35.8206
17	14.2754	-0.0245	3.0504	4.5428	0.2063	10.7431	0.0025	-0.0675	0.3448	-0.5937	0.3051	0.2113	-0.6873	0.3512	-0.3076	-0.1007	-0.0899	-0.0091	-0.2261	0.1098	-0.2065	4.3122	35.0583	18.0846
18	8.8589	9.8891	-2.2718	29.7451	-4.6676	12.7994	0.4837	-0.3096	1.0189	0.0466	-0.4341	-0.1982	-0.5893	-0.0776	-0.0496	-0.2111	-0.0811	-0.0482	-0.1626	0.0321	-0.0457	19.8816	48.0392	18.6392
19	11.1508	3.2881	-2.1724	9.0078	-1.3176	7.7455	-0.0963	0.6359	-0.0917	-0.4161	0.1488	-0.0044	0.7951	0.0662	-0.0525	-0.0557	-0.0569	-0.0068	-0.2935	-0.0172	-0.2764	3.6201	5.6196	27.2723
20	10.5002	-13.0242	-5.4295	19.9692	9.9435	15.2352	1.0005	1.36	-0.1301	-1.6839	-1.3308	-0.2768	1.9012	0.0759	0.3303	0.4366	0.0758	0.1976	0.3188	-0.0877	0.0634	18.7705	-1.802	16.8218
21	2.2041	0.3832	-0.1836	5.9118	0.2095	15.3347	-0.1075	0.3004	-0.1035	-0.7095	0.4641	0.0733	-0.206	0.3606	-0.3566	-0.1577	-0.1119	0.0085	-0.3369	-0.0263	-0.1852	-4.7956	8.1587	28.6584
22	9.4022	4.4138	-3.1404	14.6532	-3.6899	6.8367	-0.4094	-0.2775	-0.3503	-0.0101	0.4187	0.3055	1.0821	-0.0805	-0.0092	-0.1439	0.1132	0.0803	-0.2737	-0.0235	-0.1893	-9.0413	-1.6661	45.7213
23	10.6317	-6.8164	1.9707	12.4038	-7.4089	11.0656	-0.2379	0.4074	-0.7287	0.0433	-0.0639	0.9829	-0.0111	0.2253	0.3018	-0.0993	-0.1892	0.0259	-0.3135	-0.0218	-0.2744	-1.0454	9.6616	20.8789
24	70.5193	13.9202	27.2293	30.4576	-6.3151	15.4457	-0.3035	2.9482	-1.5399	-0.6792	2.9894	3.9711	1.1429	-1.5405	-2.6859	0.0162	-0.3131	-0.2431	0.4934	0.2493	0.5383	-15.3062	14.645	12.456

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 9
2	X-RAY DIFFRACTION	1	A	36 - 53
3	X-RAY DIFFRACTION	2	A	10 - 35
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