PDB-3d3b: Structural and functional analysis of the E. coli NusB-S10 transc...

ID or keywords:

Entry

Database: PDB / ID: 3d3b

Title

Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.

Components

30S ribosomal protein S10
N utilization substance protein B

Keywords

TRANSCRIPTION / NusB / S10 / NusE / Nut site / phage lambda / lambdaN antitermination / rrn antitermination / transcription control / RNA-binding / Transcription regulation / Transcription termination / Ribonucleoprotein / Ribosomal protein

Function / homology

Function and homology information

transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Luo, X. / Wahl, M.C.

Citation

Journal: Mol.Cell / Year: 2008
Title: Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
Authors: Luo, X. / Hsiao, H.H. / Bubunenko, M. / Weber, G. / Court, D.L. / Gottesman, M.E. / Urlaub, H. / Wahl, M.C.

History

Deposition	May 9, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 13, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Aug 2, 2017	Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3d3b.cif.gz	75.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3d3b.ent.gz	55.4 KB	Display	PDB format
PDBx/mmJSON format	3d3b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3d3b_validation.pdf.gz	449.3 KB	Display	wwPDB validaton report
Full document	3d3b_full_validation.pdf.gz	453.3 KB	Display
Data in XML	3d3b_validation.xml.gz	15.9 KB	Display
Data in CIF	3d3b_validation.cif.gz	23.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3b ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3b	HTTPS FTP

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Related structure data

Related structure data	3d3cC 1j5eS 1tzvS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3u5p-8 2ddb-1 2yt4-d 2ham-d 3mz8-2 2ddb-4 1y0x-d 2epf-3 3mz8-1 1xx5-1 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
Related items in Molecule of the Month	#157 - Jan 2013 Transfer-Messenger RNA similarity (1) #253 - Jan 2021 Expressome similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1)

Deposited unit

A: N utilization substance protein B

J: 30S ribosomal protein S10

hetero molecules

26.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	40.740, 48.990, 112.770
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	N utilization substance protein B / Protein nusB Mass: 15838.095 Da / Num. of mol.: 1 / Mutation: K2E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nusB, ssyB, b0416, JW0406 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A780
#2: Protein	30S ribosomal protein S10 Mass: 9608.144 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsJ, nusE, b3321, JW3283 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A7R5
#3: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₇NO₃S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUES 46-67 OF CHAIN J ARE REPLACED WITH A SINGLE SER.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.1 M CHES, pH 8.8, 18 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9051 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2006 / Details: mirrors
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9051 Å / Relative weight: 1
Reflection	Resolution: 1.3→30 Å / Num. all: 56411 / Num. obs: 56411 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Net I/σ(I): 17.5
Reflection shell	Resolution: 1.3→1.4 Å / Redundancy: 14.6 % / R_merge(I) obs: 0.648 / Mean I/σ(I) obs: 5.3 / R_sym value: 0.648 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345dtb		data collection
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ID 1TZV and PDB ID 1J5E (chain J)

1tzv

1j5e

Resolution: 1.3→20 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.966 / SU B: 1.648 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20448	2820	5 %	RANDOM
R_work	0.17348	-	-	-
obs	0.17504	53574	100 %	-
all	-	56394	-	-

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: 24.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.34 Å²	0 Å²	0 Å²
2-	-	0.19 Å²	0 Å²
3-	-	-	-0.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1779	0	39	316	2134

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2096
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.512	2.001	2867
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.737	5	277
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.796	23.407	91
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.893	15	378
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.802	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	329
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1597
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	1110
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	1472
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	243
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	0.166	0.2	77
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.161	0.2	35
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	0.854	1.5	1335
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.312	2	2139
X-RAY DIFFRACTION	r_scbond_it	2.472	3	819
X-RAY DIFFRACTION	r_scangle_it	3.575	4.5	728
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.3→1.334 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	205	-
R_work	0.278	3904	-
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	7.2488	0.9298	1.8827	1.2383	0.2805	2.2981	-0.0356	0.0707	0.1431	0.0145	-0.0321	0.075	0.0011	-0.0747	0.0677	-0.0314	-0.0001	0.0013	-0.0148	0.0017	-0.022	3.816	0.294	-19.006
2	2.5345	1.5847	0.6543	3.8617	0.4279	3.4356	-0.0382	0.0277	-0.0214	-0.0425	0.0221	0.0038	0.0229	0.2283	0.0161	-0.0224	-0.0026	0.0029	-0.0029	-0.0029	-0.0267	11.682	-5.26	-25.065
3	11.2182	-6.6264	3.8229	13.8888	-2.7668	1.3287	0.0542	-0.2905	-0.3534	-0.1376	-0.025	0.3481	0.1541	-0.2454	-0.0292	0.0214	-0.0564	0.0031	0.0153	-0.0236	-0.0212	-1.427	-10.015	-23.923
4	1.7077	0.4677	0.1528	4.8401	1.9489	2.2055	-0.0012	0.2524	0.0909	-0.1662	0.0396	-0.0163	-0.146	0.0054	-0.0384	-0.0045	0.0105	-0.0053	-0.0119	0.0109	-0.0241	3.991	3.023	-26.847
5	3.1959	2.4183	-2.0376	11.0592	5.7247	14.305	0.216	-0.1368	0.4609	0.6519	-0.1873	-0.0138	-0.3777	0.1333	-0.0287	0.0796	-0.037	-0.0086	-0.0749	-0.0212	0.0817	8.104	17.267	-14.404
6	2.526	3.876	0.4127	15.899	16.7197	26.0705	0.3774	-0.142	0.1696	-0.4766	-0.6512	0.593	-0.8058	-0.5512	0.2739	0.0623	0.0169	-0.0817	-0.0092	-0.0578	0.0542	10.132	13.737	-1.103
7	2.8964	-1.1902	2.8258	1.9337	-1.5635	3.6647	-0.0399	-0.0224	0.0622	0.0076	0.0127	-0.0968	-0.0877	-0.0032	0.0272	-0.0093	0.0202	-0.0021	-0.0196	0.0101	-0.0203	3.083	9.707	-17.526
8	1.8341	-1.7801	1.5218	3.2407	-2.4325	2.9163	-0.1133	-0.2211	-0.1091	0.0443	0.1785	0.0997	-0.0403	-0.1557	-0.0652	-0.019	0.0215	0.0012	0.0036	0.0119	-0.0101	-5.33	6.117	-13.934
9	1.9542	-0.6919	0.6656	2.2479	-1.6204	4.3014	-0.1422	-0.2827	0.0397	0.2214	0.0829	-0.0161	-0.2153	-0.1352	0.0593	-0.0026	0.0419	-0.0022	0.0167	-0.0302	-0.0302	-4.183	15.065	-11.311
10	13.7408	-5.8849	-1.8543	5.1735	3.2232	2.4743	0.0759	0.11	-0.0951	0.3069	-0.051	-0.0673	0.5507	-0.2619	-0.0249	0.1342	0.0888	0.01	0.0943	-0.0223	0.0464	27.254	-22.062	-17.914
11	5.0745	-4.1313	-5.9821	5.0122	6.2758	10.3002	-0.0775	0.0438	-0.1055	0.0849	-0.059	0.0431	0.2874	-0.1316	0.1365	-0.0124	0.0137	0.0071	-0.0199	0.0161	-0.0199	13.215	-12.197	-7.571
12	9.4734	-2.8947	-7.1019	2.1065	2.6259	7.049	0.1084	0.0896	0.2542	-0.0242	-0.0713	-0.2323	-0.2453	0.0919	-0.0371	-0.0349	-0.0154	-0.0096	-0.0022	0.0285	0.0069	19.486	-2.517	-7.401
13	3.4446	-0.1174	-1.7817	0.8007	-0.6418	2.6576	0.0586	0.1732	-0.0503	-0.0294	-0.0531	0.0516	0.0143	-0.0751	-0.0056	-0.0277	-0.0042	-0.0022	-0.019	0.0092	-0.0175	9.139	-7.161	-10.608
14	4.2449	-1.8207	-2.9408	1.4661	1.6931	4.3446	-0.0507	0.0745	-0.0692	-0.0132	-0.0536	-0.0274	0.0805	0.0671	0.1044	-0.0246	0.0097	0.0095	-0.0105	0.0324	-0.0136	14.28	-9.672	-11.405
15	6.8056	-0.1978	6.2574	1.4408	2.5835	16.2339	0.1469	0.7981	0.1804	0.1301	-0.2098	-0.1911	0.58	1.3508	0.0629	-0.0296	0.0789	0.0147	0.1348	0.0676	-0.0105	29.839	-12.38	-8.994
16	123.1557	-11.9976	-31.8314	1.1705	3.2217	16.7337	0.5171	-0.4843	-0.1199	0.386	-0.1268	-0.2188	-0.3848	-0.2516	-0.3903	0.0193	0.0291	-0.0586	0.0118	-0.0105	0.1022	20.705	-6.651	2.146
17	5.4761	-6.2714	-8.8844	10.1945	12.9497	19.5938	-0.2745	-0.0659	-0.1826	0.1282	0.0682	0.0261	0.5148	0.1884	0.2063	-0.0008	0.0422	0.0098	-0.0133	0.0329	-0.021	16.84	-15.649	-6.091

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	1 - 25	3 - 27
2	X-RAY DIFFRACTION	2	A	A	26 - 38	28 - 40
3	X-RAY DIFFRACTION	3	A	A	39 - 43	41 - 45
4	X-RAY DIFFRACTION	4	A	A	44 - 57	46 - 59
5	X-RAY DIFFRACTION	5	A	A	58 - 71	60 - 73
6	X-RAY DIFFRACTION	6	A	A	72 - 77	74 - 79
7	X-RAY DIFFRACTION	7	A	A	78 - 96	80 - 98
8	X-RAY DIFFRACTION	8	A	A	97 - 116	99 - 118
9	X-RAY DIFFRACTION	9	A	A	117 - 139	119 - 141
10	X-RAY DIFFRACTION	10	J	B	-4 - 4	1 - 9
11	X-RAY DIFFRACTION	11	J	B	5 - 13	10 - 18
12	X-RAY DIFFRACTION	12	J	B	14 - 33	19 - 38
13	X-RAY DIFFRACTION	13	J	B	34 - 47	39 - 52
14	X-RAY DIFFRACTION	14	J	B	48 - 58	53 - 63
15	X-RAY DIFFRACTION	15	J	B	59 - 69	64 - 74
16	X-RAY DIFFRACTION	16	J	B	70 - 74	75 - 79
17	X-RAY DIFFRACTION	17	J	B	75 - 82	80 - 87

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