PDB-5uxx: Co-crystal structure of the sigma factor RpoE in complex with the...

ID or keywords:

Entry

Database: PDB / ID: 5uxx

Title

Co-crystal structure of the sigma factor RpoE in complex with the anti-sigma factor NepR from Bartonella quintana

Components

Anti-sigma factor NepR
RNA polymerase sigma factor

Keywords

dna binding protein/unknown function / SSGCID / Bartonella quintana / sigma factor / anti-sigma factor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / dna binding protein-unknown function complex

Function / homology

Function and homology information

sigma factor activity / DNA-templated transcription initiation / DNA binding
Similarity search - Function

Biological species

Bartonella quintana (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.45 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Co-crystal structure of the sigma factor RpoE in complex with the anti-sigma factor NepR from Bartonella quintana
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fairman, J.W. / Dranow, D.M. / Sullivan, A.H. / Lorimer, D. / Edwards, T.E.

History

Deposition	Feb 23, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uxx.cif.gz	182 KB	Display	PDBx/mmCIF format
PDB format	pdb5uxx.ent.gz	146 KB	Display	PDB format
PDBx/mmJSON format	5uxx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uxx_validation.pdf.gz	452.4 KB	Display	wwPDB validaton report
Full document	5uxx_full_validation.pdf.gz	454.5 KB	Display
Data in XML	5uxx_validation.xml.gz	17.9 KB	Display
Data in CIF	5uxx_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/5uxx ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5uxx	HTTPS FTP

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Related structure data

Related structure data	4qic 5uxv 5uxw
Similar structure data	6mi6-3 5naa-2 5npj-1 5whg-d 6mi6-1 2grk-1 7e2m-1 3czz-d 4llv-1 6a5w-2 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
Other databases	TargetTrack: SSGCID-BAQUA.17208.A TargetTrack: SSGCID-BAQUA.17842.A

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (5)

Deposited unit

A: RNA polymerase sigma factor

B: Anti-sigma factor NepR

C: RNA polymerase sigma factor

D: Anti-sigma factor NepR

hetero molecules

53.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA polymerase sigma factor

B: Anti-sigma factor NepR

hetero molecules

defined by author&software
Evidence: gel filtration, Runs as a heterodimer of RpoE and NepR on a gel.
26.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: RNA polymerase sigma factor

D: Anti-sigma factor NepR

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.420, 92.420, 127.740
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A
2	1	1	CHAIN C
1	1	2	CHAIN B
2	1	2	CHAIN D

NCS ensembles :

ID
1
2

#1: Protein	RNA polymerase sigma factor Mass: 18753.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: sigH, BQ10960 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3M3R8
#2: Protein	Anti-sigma factor NepR Mass: 7831.784 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella quintana (strain Toulouse) (bacteria) Strain: Toulouse / Gene: BQ10970, BQ10970 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3LV19
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 62.26 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: BaquA.17208.a.CB1.PS01985 at 24.97mg/ml was mixed 1:1 with a condition based on MCSG2(b11): 29% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris/HCl, pH = 7.2.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 16, 2014
Radiation	Monochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.45→46.21 Å / Num. obs: 44774 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.75 % / B_iso Wilson estimate: 30.56 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 10.75
Reflection shell	Resolution: 2.45→2.51 Å / R_merge(I) obs: 0.516 / Mean I/σ(I) obs: 2.71 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
RESOLVE		phasing
PHENIX		phasing
PHENIX	dev_1738	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.45→46.21 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 21.35

	R_factor	Num. reflection	% reflection
R_free	0.223	2182	4.87 %
R_work	0.191	-	-
obs	0.192	44764	99.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 41.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→46.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3212	0	15	154	3381

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3282
X-RAY DIFFRACTION	f_angle_d	0.523	4426
X-RAY DIFFRACTION	f_dihedral_angle_d	13.547	1210
X-RAY DIFFRACTION	f_chiral_restr	0.019	504
X-RAY DIFFRACTION	f_plane_restr	0.002	573

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	1360	X-RAY DIFFRACTION	POSITIONAL
1	2	C	1360	X-RAY DIFFRACTION	POSITIONAL
2	1	B	398	X-RAY DIFFRACTION	POSITIONAL
2	2	D	398	X-RAY DIFFRACTION	POSITIONAL

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4501-2.5034	0.2679	164	0.2649	2681	X-RAY DIFFRACTION	100
2.5034-2.5616	0.2537	176	0.2569	2641	X-RAY DIFFRACTION	100
2.5616-2.6257	0.3036	114	0.2538	2662	X-RAY DIFFRACTION	100
2.6257-2.6966	0.2583	150	0.2427	2607	X-RAY DIFFRACTION	100
2.6966-2.776	0.2983	114	0.2355	2719	X-RAY DIFFRACTION	100
2.776-2.8656	0.2751	154	0.225	2610	X-RAY DIFFRACTION	100
2.8656-2.968	0.2392	132	0.2212	2706	X-RAY DIFFRACTION	100
2.968-3.0868	0.2367	152	0.2124	2640	X-RAY DIFFRACTION	100
3.0868-3.2272	0.222	102	0.2108	2653	X-RAY DIFFRACTION	100
3.2272-3.3973	0.277	146	0.1984	2663	X-RAY DIFFRACTION	100
3.3973-3.6101	0.1814	114	0.1786	2659	X-RAY DIFFRACTION	100
3.6101-3.8887	0.1896	132	0.1592	2690	X-RAY DIFFRACTION	100
3.8887-4.2798	0.2062	110	0.1539	2680	X-RAY DIFFRACTION	100
4.2798-4.8985	0.1791	131	0.1535	2681	X-RAY DIFFRACTION	100
4.8985-6.1693	0.2221	156	0.1909	2647	X-RAY DIFFRACTION	100
6.1693-46.2182	0.1805	135	0.1565	2643	X-RAY DIFFRACTION	99

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	7.9916	-0.5629	-1.3538	4.2337	0.4469	4.7472	0.0083	-0.1297	-0.3565	0.3225	-0.1519	-0.0603	0.0745	-0.0358	0.1828	0.2986	-0.0585	-0.0466	0.1753	0.043	0.2161	58.9841	182.4484	15.9955
2	7.6094	-4.2062	-4.6536	9.3023	6.4342	5.1524	-0.1383	-0.3682	-0.5997	0.4814	0.0455	0.2319	0.84	0.2271	0.2	0.3522	-0.065	-0.0524	0.3166	0.0745	0.3267	56.4666	173.9328	12.9126
3	5.6512	1.611	-1.6803	6.3059	5.4122	6.4877	-0.3969	0.63	-0.3333	-1.0538	1.0059	-1.5899	-0.087	0.1292	-0.3847	0.4795	-0.0769	0.0027	0.2838	0.001	0.4284	64.4786	179.2521	-0.6563
4	2.3393	0.0853	-3.0821	2.292	0.2766	4.0865	-0.1598	0.7077	-0.6015	0.0193	-0.1545	0.6567	0.3335	-0.8576	0.2527	0.2501	-0.0695	0.0011	0.3278	-0.043	0.3994	46.5865	180.8349	10.7194
5	5.8925	5.1556	5.7351	4.6032	5.6813	9.0142	-0.0769	0.9899	-0.5422	0.2145	-0.0267	0.4631	0.4901	-0.5976	0.1745	0.4721	0.0543	0.0652	0.7347	-0.113	0.8354	34.9411	184.982	22.0827
6	4.69	1.1962	0.2264	1.5914	0.573	4.6542	0.0169	-0.0616	0.0858	0.1616	-0.017	0.3602	0.228	-0.3112	0.0045	0.2137	-0.0142	0.023	0.1482	0.0036	0.2667	51.5965	195.1566	13.6163
7	4.2925	-0.5379	-1.8812	8.3241	6.5209	7.3788	0.1778	-0.1971	0.4968	-0.2325	0.1643	0.505	-0.8378	-0.7403	-0.1014	0.2772	-0.0027	-0.0195	0.3443	0.1081	0.4799	47.6254	203.2403	8.055
8	3.8034	-0.2091	1.397	2.9506	-0.6921	2.7575	-0.0454	0.2522	-0.0037	-0.4663	0.2193	0.1331	0.1178	-0.0689	-0.1662	0.2828	-0.0585	0.0229	0.2721	0.0443	0.1933	65.4358	202.2146	-0.5544
9	3.9386	1.3897	5.8532	3.981	1.3902	9.1349	-0.5716	0.6214	1.0031	-0.1244	-0.1368	-0.0491	-0.3712	0.8084	0.6099	0.2725	-0.0356	0.0486	0.3407	0.0108	0.4138	76.1271	207.2131	0.4157
10	4.1595	6.2872	-4.6865	9.5369	-7.0972	5.289	-0.7343	0.8548	-0.2053	-1.4371	1.204	-0.7319	0.4701	-0.4688	-0.5972	0.8012	-0.1973	0.1004	0.589	-0.069	0.3936	66.58	193.2528	-9.2823
11	6.659	3.6054	-0.0817	4.7439	-0.6392	3.3349	-0.3865	0.3031	-0.6687	-0.3315	0.2025	-0.9335	-0.0422	0.7929	0.158	0.2753	-0.0212	0.0571	0.4228	-0.0277	0.3572	82.3152	199.9069	-0.0299
12	8.8911	-2.5196	-3.8695	6.2991	2.7425	6.3822	-0.3518	1.0149	0.3298	-1.0967	0.349	-0.2525	-0.2738	0.5645	0.0677	0.6269	-0.0117	-0.014	0.69	-0.0572	0.4051	93.4742	208.2457	8.8202
13	4.6728	0.7028	-1.6908	3.4455	1.417	3.8587	0.1959	0.3399	0.3402	0.2251	-0.1322	-0.4067	-0.4279	0.061	-0.0497	0.2848	-0.0564	-0.0648	0.3544	-0.0674	0.3424	77.0383	203.134	20.6221
14	6.9191	0.0626	-1.1649	8.3518	-0.7436	8.1345	-0.0741	0.0357	-0.2802	-0.3621	0.1298	-0.2999	-0.3614	0.1459	-0.0808	0.1848	-0.001	-0.0048	0.2234	-0.0531	0.2655	76.4698	188.995	7.4548
15	4.561	3.5501	2.6397	3.5399	3.5762	4.3224	0.2608	-0.482	-0.7581	0.92	0.0039	-0.9123	1.2738	0.4551	-0.4156	0.3434	-0.0029	-0.0847	0.3637	0.0739	0.6183	81.5916	186.1774	16.2156
16	6.3724	3.9033	-0.4539	5.9688	-0.9109	0.2893	0.4059	-0.6486	-0.7388	0.2002	0.0115	0.1554	1.304	-0.0695	-0.2924	0.816	-0.2189	0.0557	0.7983	-0.0841	0.3907	77.9491	190.867	28.8194
17	1.6233	-1.464	1.8442	6.5678	-5.7167	6.8166	0.0244	0.0678	0.2093	0.0234	-0.0404	-0.0271	-0.1177	-0.0379	0.0206	0.173	-0.0139	0.0411	0.2402	-0.0239	0.2744	58.5174	200.1073	14.686
18	6.5437	-1.3857	0.1235	8.9583	7.7645	8.9667	0.1974	0.3198	-0.1408	0.7616	0.279	-0.3987	0.9104	-0.041	-0.4292	0.5776	-0.0093	-0.1519	0.3811	0.1046	0.4082	64.2313	169.4645	18.9236
19	4.955	-3.3886	-0.0491	3.3071	-1.502	2.9444	0.0997	-0.4014	-0.2964	-0.0508	0.011	0.3092	0.3069	-0.2038	-0.0605	0.2451	-0.0856	-0.0479	0.3044	-0.0077	0.2892	70.1021	193.1002	19.4052
20	3.3577	1.2681	-0.5922	5.1262	-2.7605	2.1705	-0.3232	0.4708	0.0994	-0.2659	0.5034	0.1739	-0.3266	0.4103	-0.1804	0.2675	-0.0753	0.0151	0.3511	0.0389	0.2901	65.6155	212.1313	-2.8926
21	3.1891	2.3122	-0.1352	4.3937	-3.2203	3.8329	-0.6532	-0.4555	0.3496	-0.628	0.228	-0.1976	1.1454	0.1713	0.4228	0.6425	-0.0696	0.0109	1.212	0.1797	0.3783	68.2312	209.8165	-17.6671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 5 THROUGH 32 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 33 THROUGH 50 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 51 THROUGH 56 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 57 THROUGH 81 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 82 THROUGH 91 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 92 THROUGH 141 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 142 THROUGH 164 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 2 THROUGH 26 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 27 THROUGH 46 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 47 THROUGH 56 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 57 THROUGH 81 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 82 THROUGH 91 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 92 THROUGH 114 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 115 THROUGH 141 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 142 THROUGH 159 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 160 THROUGH 164 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 15 THROUGH 43 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 44 THROUGH 60 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 17 THROUGH 39 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 40 THROUGH 58 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 59 THROUGH 64 )

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