PDB-4omz: Crystal Structure of NolR from Sinorhizobium fredii

ID or keywords:

Entry

Database: PDB / ID: 4omz

Title

Crystal Structure of NolR from Sinorhizobium fredii

Components

NolR

Keywords

TRANSCRIPTION / helix-turn-helix / transcription regulator

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Sinorhizobium fredii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.64 Å

Authors

Lee, S.G. / Krishnan, H.B. / Jez, J.M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.
Authors: Lee, S.G. / Krishnan, H.B. / Jez, J.M.

History

Deposition	Jan 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 4, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4omz.cif.gz	313 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4omz_validation.pdf.gz	494.9 KB	Display	wwPDB validaton report
Full document	4omz_full_validation.pdf.gz	504.1 KB	Display
Data in XML	4omz_validation.xml.gz	31.6 KB	Display
Data in CIF	4omz_validation.cif.gz	44.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/4omz ftp://data.pdbj.org/pub/pdb/validation_reports/om/4omz	HTTPS FTP

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Related structure data

Related structure data	4omyC 4on0C C: citing same article (ref.)
Similar structure data	1u2w-1 3jth-d 3b57-d 4po4-2 3cuo-1 2zkz-2 6ts0-d 2z5q-d 5e1u-d 6o8k-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4omyC

4on0C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NolR

B: NolR

C: NolR

D: NolR

E: NolR

F: NolR

G: NolR

H: NolR

hetero molecules

103 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NolR

B: NolR

hetero molecules

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

2

C: NolR

D: NolR

hetero molecules

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

3

E: NolR

F: NolR

hetero molecules

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

4

G: NolR

H: NolR

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.771, 99.619, 113.017
Angle α, β, γ (deg.)	90.00, 90.08, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	F-322- HOH

#1: Protein	NolR Mass: 12745.669 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium fredii (bacteria) / Gene: nolR / Production host: Escherichia coli (E. coli) / References: UniProt: Q83TD2
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.75 Å³/Da / Density % sol: 55.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 1.6 M sodium phosphate monobasic/0.4 M potassium phosphate dibasic, 0.1 M sodium phosphate dibasic/citric acid, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2013 / Details: mirrors
Radiation	Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.64→37.4 Å / Num. obs: 32349 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_sym value: 0.056 / Net I/σ(I): 17.7

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
SHELXS		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.64→37.4 Å / SU ML: 0.29 / σ(F): 1.38 / Phase error: 26.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.246	1546	5.07 %
R_work	0.203	-	-
obs	0.205	30519	93.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.64→37.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5908	0	70	243	6221

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6024
X-RAY DIFFRACTION	f_angle_d	1.105	8117
X-RAY DIFFRACTION	f_dihedral_angle_d	16.615	2261
X-RAY DIFFRACTION	f_chiral_restr	0.043	953
X-RAY DIFFRACTION	f_plane_restr	0.005	1024

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 (%)
2.6411-2.7263	0.3406	73	0.2555	1386	X-RAY DIFFRACTION	49
2.7263-2.8237	0.3188	128	0.2518	2485	X-RAY DIFFRACTION	88
2.8237-2.9367	0.2902	163	0.2279	2783	X-RAY DIFFRACTION	99
2.9367-3.0703	0.2931	141	0.2434	2771	X-RAY DIFFRACTION	100
3.0703-3.2321	0.26	145	0.2295	2800	X-RAY DIFFRACTION	100
3.2321-3.4345	0.2829	150	0.2194	2793	X-RAY DIFFRACTION	100
3.4345-3.6994	0.2293	159	0.2033	2768	X-RAY DIFFRACTION	99
3.6994-4.0713	0.1952	135	0.177	2779	X-RAY DIFFRACTION	100
4.0713-4.6595	0.229	139	0.159	2818	X-RAY DIFFRACTION	99
4.6595-5.8668	0.2087	145	0.1944	2838	X-RAY DIFFRACTION	100
5.8668-37.4258	0.24	168	0.1996	2752	X-RAY DIFFRACTION	97

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	1.8376	0.1255	1.316	3.0613	-0.2516	7.2174	0.0715	0.0318	-0.3241	-0.6866	0.2208	0.1718	0.2353	0.5579	-0.2466	0.3909	0.0543	0.0495	0.2365	-0.0091	0.4503	5.3993	-29.1798	18.8894
2	0.0354	-0.0559	0.2906	0.6658	-0.4104	2.3734	0.0558	-0.4924	0.0235	0.2373	0.0384	0.122	-0.0783	-0.0021	-0.0527	0.3594	0.0425	0.7454	0.6253	0.1279	0.3002	4.4629	-26.3563	45.9224
3	7.3518	-0.0394	1.9363	4.3891	0.4211	0.5528	0.2616	-0.9433	-0.2468	0.6743	-0.0463	0.3931	-0.111	-0.0963	-0.2463	0.4871	0.0235	0.218	0.5214	0.1615	0.7473	-0.6463	-33.6027	41.601
4	2.6327	-0.4485	1.2537	4.3702	-0.9839	2.3681	0.2601	-0.332	-0.2961	0.5654	-0.1921	0.1123	-0.1094	-0.1791	-0.1257	0.2065	0.0081	0.1164	0.2855	0.0291	0.3269	10.9146	-29.6098	40.781
5	1.1826	1.5796	1.8009	2.1103	2.4056	2.7421	-0.0887	-1.1691	-0.4838	1.4895	-0.0688	-0.4135	0.123	0.4975	0.1636	1.2643	0.1151	0.3342	0.7019	0.1062	0.6366	4.6268	-19.024	54.1425
6	1.1655	0.6001	-0.7411	1.2938	-0.0363	6.4801	-0.1905	-0.4602	0.1832	0.2559	0.2958	0.3425	-0.3148	-0.0699	0.004	0.3053	0.1559	0.1249	0.3194	-0.0354	0.3708	1.8454	-18.0892	29.1506
7	0.7063	-0.6879	-0.2367	7.601	-5.762	5.4393	-0.0999	0.0729	-0.0606	0.1691	-0.3219	-0.4347	0.03	0.6475	0.4	0.3673	0.1528	0.0846	0.4671	0.0593	0.3976	6.121	-12.1944	10.7597
8	6.0656	4.4704	2.8197	9.6873	-5.3036	9.8357	-0.0583	0.5434	-0.4468	-1.0584	0.3098	0.6801	0.6662	-0.5606	-0.2917	0.3851	-0.0009	-0.0462	0.3564	-0.0275	0.3411	-2.1358	-20.7939	8.3872
9	4.3413	-0.4058	-3.3727	1.7378	0.644	6.6145	0.0306	-0.0198	-0.0043	-0.0148	-0.153	0.6944	-0.032	-0.699	0.0676	0.2367	0.0092	0.1173	0.3648	0.1549	0.6647	-6.4969	-16.3152	17.7015
10	0.781	0.2367	-0.2548	0.9485	-0.4947	1.666	0.0413	0.1134	0.064	-0.0368	0.0028	0.1156	-0.1282	-0.0371	-0.097	0.1872	0.0976	0.1839	0.2791	-0.0494	0.3237	5.3114	-13.0497	17.8945
11	2.8524	1.0049	-1.363	4.5984	1.2117	1.3255	-0.0651	2.3462	0.3508	-2.0325	-0.1225	0.3899	-1.4558	-1.0725	0.1789	0.9013	0.1103	0.1065	1.2729	0.0247	0.5858	34.0408	-35.7298	33.0981
12	3.3655	-0.2857	-1.1943	3.2098	1.6736	7.0171	0.1911	0.0003	-0.406	0.2364	0.0218	-0.3575	-0.1087	-0.1037	-0.1119	0.2803	-0.0802	0.0092	0.2259	0.1088	0.3705	36.2734	-35.7214	59.0488
13	5.1681	2.2962	1.8658	1.153	1.5279	4.3421	-0.0821	-0.3021	-0.2681	0.3715	0.3047	0.2118	0.1681	-0.2592	-0.1632	0.7516	-0.0278	-0.164	0.6099	0.3016	0.4729	37.2477	-37.2725	78.8765
14	2.9227	1.0237	1.1207	1.7789	0.9094	3.8454	-0.1503	-0.4685	-0.5639	0.4585	0.2763	-0.3708	0.4881	-0.1906	-0.0233	0.3222	0.0372	-0.0023	0.2563	0.1233	0.4137	39.3461	-33.2241	69.2825
15	4.162	-2.2491	-2.6349	3.1168	-0.7164	4.8331	-0.1368	-2.3014	0.1542	1.5213	-0.1643	-0.2615	-0.4536	0.2608	0.2901	1.0171	-0.2082	0.0166	1.3649	0.173	0.5001	28.0295	-35.8892	82.3426
16	3.0299	-0.218	0.4772	2.6593	1.3545	4.9755	0.157	-0.2636	-0.3438	0.3476	-0.1821	0.2506	0.0789	-0.0914	-0.007	0.1881	-0.1336	0.0605	0.3019	0.0199	0.3408	26.7606	-38.5944	56.4029
17	7.4939	0.7315	3.868	1.1483	1.3765	6.7373	-0.0488	0.7948	-0.0862	-0.3904	0.3634	-0.4854	-0.3042	0.4524	-0.2556	0.3244	-0.1255	0.0832	0.3925	0.0011	0.3745	26.9869	-40.9643	36.5828
18	2.8206	1.1606	1.5579	1.1267	0.7397	2.5147	0.1306	-0.0385	-0.4573	-0.124	-0.0055	-0.1542	0.253	-0.1837	-0.109	0.22	-0.0575	0.0838	0.1974	0.1025	0.3833	22.7881	-38.9563	46.093
19	1.2315	-0.9856	0.5916	1.8855	-0.6527	7.768	-0.1685	0.8365	-0.0327	-0.9267	0.1322	0.4527	0.4798	-0.0524	-0.0129	0.5631	-0.3151	-0.1434	0.5867	-0.0122	0.4571	2.1146	-65.3284	15.3267
20	3.0057	2.5241	-3.2812	5.2213	-2.8985	3.7525	0.4934	-0.377	0.5008	0.7359	-0.0628	0.1078	-0.3086	0.1631	-0.3065	0.2974	-0.0285	0.0261	0.2298	0.0271	0.3768	1.6963	-62.5249	43.465
21	2.3448	-2.1498	1.9036	2.7946	-1.9393	1.631	-0.0268	-0.1331	0.0332	0.2679	0.2735	0.7227	0.1259	-0.3888	-0.3876	0.2564	-0.0632	0.0195	0.384	0.0955	0.6752	-6.7664	-65.6273	38.8196
22	1.086	0.4701	-0.5621	2.9961	-2.2242	3.3812	0.1239	-0.0511	-0.0687	0.0281	0.0124	0.2371	0.1609	-0.0886	-0.073	0.1675	-0.0622	-0.0792	0.1998	0.0068	0.2926	5.2719	-68.8783	38.5913
23	2.3717	-0.3246	-0.4538	3.7655	1.6021	8.4334	0.0082	0.1924	0.1262	0.2985	0.1436	0.4179	0.028	0.1192	-0.0856	0.1751	-0.081	-0.1069	0.2952	0.0413	0.3885	5.2643	-54.6222	28.3761
24	0.9316	0.1516	0.9668	0.9748	0.8424	2.2742	0.0103	-0.2737	-0.1154	0.1007	0.0299	-0.0458	0.0858	0.0997	-0.0214	0.553	-0.014	-0.311	0.7008	0.1345	0.302	3.8899	-53.6365	5.8913
25	1.4228	1.0766	-0.8261	3.3426	-1.5151	1.9658	0.2015	0.3714	0.4862	-0.6615	-0.0409	0.55	0.0918	-0.4378	-0.0092	0.2266	0.0204	-0.0794	0.4059	0.0438	0.3601	7.742	-51.187	15.4952
26	0.6651	-1.1954	-2.0175	5.2616	0.6985	8.8652	0.0117	-2.2864	-0.3028	1.426	0.2007	0.2164	0.9324	-1.0937	-0.2374	0.6645	-0.14	-0.2283	1.2861	0.0186	0.5744	34.2362	-46.558	23.0606
27	3.7161	-0.5425	-3.9538	3.3293	2.6676	5.5515	-0.0061	-0.5763	0.3667	0.1077	-0.0018	-0.9566	0.2559	1.069	-0.0449	0.2838	0.0739	-0.0236	0.2804	0.0177	0.4915	38.7362	-46.3001	6.4681
28	2.2918	-0.2647	-0.4257	1.6669	-1.7534	4.6221	-0.0237	0.1239	-0.0578	-0.5865	0.0885	0.2221	-0.0155	-0.1843	0.0117	0.517	0.024	0.0372	0.2686	0.3037	0.337	33.5732	-46.1278	-13.3792
29	5.8003	-2.5583	-1.9494	1.153	1.2131	5.4001	-0.0169	0.483	0.4405	-0.3993	0.1849	-0.0113	-0.2294	-0.2825	-0.1364	0.6171	0.0437	0.2206	0.5674	0.2667	0.3848	37.3474	-44.6301	-22.352
30	3.4135	0.3239	0.6325	5.1036	0.6292	2.7707	-0.0987	0.6826	0.7345	-0.609	0.0427	-0.316	-0.7994	0.2885	0.0625	0.5517	-0.0868	0.163	0.3433	0.2078	0.7326	42.7311	-40.0364	-13.3176
31	3.332	-0.7862	-0.5047	1.0425	0.0706	3.8201	-0.262	0.3449	-0.0355	-0.5214	0.1179	-0.2994	-0.1176	-0.0451	0.0952	0.3165	-0.0439	0.1244	0.1861	0.0401	0.3549	38.85	-51.7584	-12.5225
32	2.9395	0.2036	-0.3934	2.7109	0.1659	9.9039	-0.0535	0.8066	0.4191	-0.8894	-0.2633	0.1774	-0.7201	-1.185	0.2763	0.4306	0.1946	0.0243	0.5385	0.1096	0.4572	25.2281	-42.9333	-11.9744
33	4.5156	-1.1852	-3.7077	1.7292	3.3841	9.4289	0.1008	-0.5798	0.2821	0.397	0.3077	-0.302	0.1624	0.2027	-0.3208	0.2704	0.0346	-0.0022	0.3393	0	0.3511	28.269	-42.7602	15.2949
34	3.7308	-0.0389	-1.8328	2.6765	0.8511	3.0112	0.2727	0.0445	0.8296	0.1834	0.0484	0.0682	-0.4784	-0.1108	-0.3394	0.2949	0.0955	0.0906	0.2605	0.0686	0.4723	19.8904	-38.2818	13.327
35	7.6579	0.4328	-3.2366	3.2466	1.871	4.0647	-0.2636	-0.1644	-0.2783	0.2826	0.1577	-0.1354	0.4462	0.0199	0.0812	0.2013	0.0402	0.0283	0.2272	0.1145	0.2545	29.5406	-53.7506	3.7845

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 103 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 9 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 10 through 38 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 39 through 44 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 55 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 56 through 68 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 69 through 102 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 5 through 9 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 10 through 40 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 41 through 55 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 56 through 104 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 5 through 9 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 10 through 40 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 41 through 55 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 56 through 102 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 5 through 26 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 27 through 55 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 56 through 68 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 69 through 102 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 6 through 40 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 41 through 55 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 56 through 103 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 5 through 9 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 10 through 26 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 27 through 40 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 41 through 55 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 56 through 68 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 69 through 102 )
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 6 through 26 )
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 27 through 55 )
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 56 through 87 )
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 88 through 102 )

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