PDB-7v5v: LysR family transcriptional regulator RipR from Salmonella Typhimurium

ID or keywords:

Entry

Database: PDB / ID: 7v5v

Title

LysR family transcriptional regulator RipR from Salmonella Typhimurium

Components

RipR

Keywords

TRANSCRIPTION / host-pathogen interaction

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Enteritidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Ki, N. / Ha, N.-C.

Funding support

1items

Citation

Journal: To Be Published
Title: The activation mechanism of the itaconic acid-responsive LTTR RipR in the pathogenesis of the foodborne-pathogen Salmonella enterica
Authors: Ki, N.

History

Deposition	Aug 18, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 24, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	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	7v5v.cif.gz	319.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7v5v.ent.gz	261.4 KB	Display	PDB format
PDBx/mmJSON format	7v5v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7v5v_validation.pdf.gz	460.5 KB	Display	wwPDB validaton report
Full document	7v5v_full_validation.pdf.gz	470.7 KB	Display
Data in XML	7v5v_validation.xml.gz	28.8 KB	Display
Data in CIF	7v5v_validation.cif.gz	39.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v5/7v5v ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v5v	HTTPS FTP

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Related structure data

Related structure data	7xroC 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

Deposited unit

A: RipR

B: RipR

C: RipR

D: RipR

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

1

A: RipR

D: RipR

defined by author&software
Evidence: gel filtration
45.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: RipR

C: RipR

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

Unit cell

Length a, b, c (Å)	66.405, 72.415, 91.612
Angle α, β, γ (deg.)	90.000, 104.620, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	RipR Mass: 22636.260 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Enteritidis (bacteria) Gene: stmR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93DX4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.34 Å³/Da / Density % sol: 47.45 %
Crystal grow	Temperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium formate pH 5.5, 19% (w/v) PEG 3,350

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Data collection

Diffraction

Mean temperature: 100.15 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 1.0448 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2021

Radiation

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

Radiation wavelength

Wavelength: 1.0448 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 42095 / % possible obs: 98.7 % / Redundancy: 6.1 % / B_iso Wilson estimate: 32.41 Å² / R_merge(I) obs: 0.1 / R_pim(I) all: 0.043 / R_rim(I) all: 0.109 / Χ²: 0.959 / Net I/σ(I): 17.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	5.9	0.362	2062	0.905	0.159	0.396	0.866	98.2
2.24-2.28	5.8	0.311	2087	0.938	0.137	0.34	0.907	98.4
2.28-2.32	5.9	0.301	2075	0.939	0.133	0.33	0.925	99
2.32-2.37	5.8	0.294	2112	0.933	0.13	0.322	0.912	98.6
2.37-2.42	5.9	0.274	2072	0.941	0.12	0.3	0.914	98.7
2.42-2.48	5.9	0.254	2106	0.948	0.112	0.278	0.986	98.7
2.48-2.54	5.7	0.226	2103	0.959	0.101	0.248	1	98.9
2.54-2.61	5.4	0.21	2089	0.962	0.099	0.233	0.974	98.9
2.61-2.69	5.6	0.182	2104	0.975	0.082	0.2	0.996	99.2
2.69-2.77	5.7	0.168	2125	0.976	0.075	0.185	1.034	98.9
2.77-2.87	6.3	0.152	2080	0.985	0.064	0.165	1.012	99.2
2.87-2.99	6.6	0.14	2145	0.985	0.058	0.152	1.04	99.3
2.99-3.12	6.5	0.129	2099	0.987	0.053	0.14	1.056	99.4
3.12-3.29	6.6	0.109	2128	0.99	0.045	0.119	1.062	99.2
3.29-3.49	6.5	0.097	2129	0.991	0.04	0.105	1.08	99.2
3.49-3.76	6.6	0.081	2088	0.994	0.033	0.088	1.079	98.6
3.76-4.14	6.4	0.07	2096	0.997	0.029	0.076	0.918	97.6
4.14-4.74	5.9	0.062	2084	0.996	0.027	0.068	0.898	97.2
4.74-5.97	6.1	0.061	2105	0.996	0.027	0.067	0.827	97.4
5.97-50	7.1	0.055	2206	0.997	0.022	0.059	0.706	99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1_4122	refinement
HKL-2000	v722	data reduction
HKL-2000	v722	data scaling
MOLREP	7.1.012	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.37→39.26 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 29.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2954	1575	4.81 %
R_work	0.2356	31185	-
obs	0.2385	32760	95.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 160.73 Å² / B_iso mean: 40.0873 Å² / B_iso min: 18.37 Å²

Refinement step

Cycle: final / Resolution: 2.37→39.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6279	0	0	30	6309
B_iso mean	-	-	-	35.84	-
Num. residues	-	-	-	-	822

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 11

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.37-2.45	0.3438	111	0.2757	2206	2317	75
2.45-2.54	0.3391	136	0.2737	2823	2959	95
2.54-2.64	0.3466	163	0.2735	2782	2945	96
2.64-2.76	0.3179	138	0.2741	2866	3004	97
2.76-2.91	0.323	152	0.2758	2889	3041	98
2.91-3.09	0.3259	135	0.2778	2870	3005	98
3.09-3.33	0.3385	149	0.268	2903	3052	98
3.33-3.66	0.3166	144	0.2453	2914	3058	98
3.66-4.19	0.2704	164	0.2131	2940	3104	99
4.19-5.28	0.2408	135	0.1901	2959	3094	100
5.28-39.26	0.2537	148	0.1997	3033	3181	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	2.0158	0.6379	1.6584	4.2038	-0.9607	4.8419	0.2087	-0.0749	-0.059	0.2008	-0.2117	0.0883	0.2959	0.1988	-0.0632	0.2206	-0.0089	0.0602	0.2592	0.0417	0.2011	14.0232	4.6279	12.1893
2	2.6543	-0.1228	3.7961	2.1265	0.0648	6.3676	-0.0168	0.1547	-0.1133	-0.0291	0.01	-0.2709	0.301	0.2479	0.0567	0.3346	-0.1246	-0.0227	0.2797	0.0044	0.2784	0.0055	-1.7537	-3.9849
3	2.0354	0.8341	1.3477	0.5416	0.2753	2.5609	-0.0144	0.2608	-0.2072	-0.2019	0.314	0.0186	0.1555	0.1738	-0.2451	0.3397	-0.0316	-0.0266	0.2283	-0.0149	0.2922	4.1382	-1.8194	-4.0811
4	8.66	-2.8248	-7.3094	4.6669	3.096	6.2957	0.9742	0.4959	0.5416	-0.3459	-0.4885	-0.1668	-0.7552	-0.4144	-0.5619	0.3898	0.0557	-0.0561	0.2908	0.0863	0.3332	29.0406	-37.7327	-48.7623
5	2.4174	-0.894	0.2123	2.6775	0.5394	0.8305	0.0127	-0.0468	0.0899	-0.254	-0.1051	-0.3173	-0.0342	0.2626	-0.0027	0.2788	-0.0563	0.0278	0.364	0.0473	0.2118	29.5696	-36.5776	-47.9496
6	2.5977	-3.2821	-0.4945	4.7199	-0.4183	2.5092	0.6258	0.2314	0.7626	-0.477	0.2896	0.5375	-0.7704	-1.239	-0.7441	0.5002	0.2148	0.1776	0.4926	0.0727	0.5874	24.4631	-25.1319	-50.5613
7	2.5825	-0.6633	-3.0238	3.0523	-0.7048	5.9603	-0.334	-0.1322	-0.2417	0.0608	0.1934	0.1006	0.7828	-0.1544	0.0321	0.3516	0.033	0.0254	0.3149	0.0938	0.1668	7.6735	-34.1603	-39.7631
8	6.7708	-1.0861	1.3877	2.6443	-0.6717	0.7031	-0.3773	-0.0194	0.5122	0.1471	0.2175	0.0954	-0.2203	-0.1906	0.1818	0.3574	0.0764	-0.0355	0.3159	-0.0112	0.2039	6.8653	-25.9489	-33.3408
9	6.482	-2.4384	-0.2914	3.625	-0.5726	2.1924	-0.0733	-0.0478	-0.0757	0.1175	0.1711	0.0237	0.1846	0.0627	-0.0462	0.2345	0.0195	-0.0122	0.1911	-0.0334	0.2069	6.7854	-35.3113	-35.1524
10	5.9337	0.7873	-1.9281	1.1697	1.5911	4.7776	-0.0335	0.5554	0.3947	-0.6095	0.5021	0.3296	0.5976	-0.1254	-0.3251	0.4747	-0.0405	0.0403	0.5004	0.1879	0.2586	28.1558	-34.2221	-58.0803
11	2.9331	-0.245	1.4373	4.2263	-1.2058	2.5325	-0.1546	-0.2649	0.2316	-0.2934	0.0446	0.2214	-0.2541	-0.0028	0.104	0.3261	0.0127	-0.0472	0.2479	0.0062	0.196	18.0548	-28.2279	-17.2989
12	1.896	-2.0035	-1.4629	6.3084	-1.0751	2.7535	-0.0331	-0.0005	0.2883	0.5501	-0.1024	-0.7318	0.0903	0.5331	0.1235	0.4035	-0.0433	-0.1196	0.3575	0.0679	0.3016	29.6822	-29.8395	-13.4458
13	3.463	0.0394	-0.3694	2.2668	0.1463	2.8478	-0.0525	-0.0108	0.1718	-0.0305	0.0116	-0.2705	0.0063	0.4085	0.0103	0.2542	0.0248	0.0118	0.2695	0.0179	0.2102	31.6775	-47.336	-31.4274
14	2.2356	-0.8922	0.3293	2.3836	1.1044	3.2228	-0.1331	-0.2158	0.1926	0.0669	0.1938	-0.1703	-0.2566	0.2508	-0.0361	0.2084	-0.0798	0.0126	0.2069	0.0229	0.1265	23.4108	-38.3402	-16.2122
15	1.3032	-0.7987	-0.7059	4.1182	1.0719	2.5949	-0.0113	0.0154	-0.2121	0.0436	0.0914	-0.3163	0.4102	0.2472	-0.0286	0.2673	-0.0205	-0.0393	0.2761	-0.018	0.264	24.425	-0.4273	-18.5068
16	0.3643	-0.1226	0.3212	2.5909	1.6299	2.8104	-0.0239	-0.0269	-0.0547	0.007	0.0417	-0.1809	0.0841	0.2363	-0.0024	0.172	-0.0128	-0.0167	0.2197	0.0259	0.2156	24.3243	13.1071	-6.9198

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 87 through 147 )	A	87 - 147
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 148 through 188 )	A	148 - 188
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 189 through 291 )	A	189 - 291
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 87 through 104 )	B	87 - 104
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 105 through 139 )	B	105 - 139
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 140 through 157 )	B	140 - 157
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 158 through 179 )	B	158 - 179
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 180 through 236 )	B	180 - 236
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 237 through 270 )	B	237 - 270
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 271 through 291 )	B	271 - 291
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 90 through 138 )	C	90 - 138
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 139 through 163 )	C	139 - 163
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 164 through 250 )	C	164 - 250
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 251 through 292 )	C	251 - 292
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 88 through 172 )	D	88 - 172
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 173 through 292 )	D	173 - 292

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