PDB-4omy: Crystal Structure of SeMet NolR from Sinorhizobium fredii in comp...

ID or keywords:

Entry

Database: PDB / ID: 4omy

Title

Crystal Structure of SeMet NolR from Sinorhizobium fredii in complex with oligo AT DNA

Components

DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 )
DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 )
NolR

Keywords

TRANSCRIPTION/DNA /

helix-turn-helix /

transcription regulator / TRANSCRIPTION-DNA complex

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Sinorhizobium fredii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.062 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4omy.cif.gz	252.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4omy.ent.gz	214.4 KB	Display	PDB format
PDBx/mmJSON format	4omy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/4omy ftp://data.pdbj.org/pub/pdb/validation_reports/om/4omy	HTTPS FTP

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Related structure data

Related structure data	4omzC 4on0C C: citing same article (ref.)
Similar structure data	4on0-1 1g5z-1 4ilu-1 1f1m-2 2ga0-4 7bml-2 2ga0-3 5kbx-d 5z2e-d 2ga0-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: NolR

B: NolR

C: NolR

D: NolR

E: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 )

F: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 )

G: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 )

H: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 )

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

1

A: NolR

B: NolR

E: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 )

F: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 )

defined by author&software
39.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: NolR

D: NolR

G: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 )

H: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 )

defined by author&software
39.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	131.019, 131.019, 67.688
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	NolR Mass: 12980.145 Da / Num. of mol.: 4 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: DNA chain	DNA (5 -D(TPAPTPTPAPGPAPGPAPAPCPCPCPTPGPAPAPGPTPTPAPA)-3 ) Mass: 6783.430 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain	DNA (5 -D(TPAPAPTPCPTPCPTPTPGPGPGPAPCPTPTPCPAPAPTPTPA)-3 ) Mass: 6716.363 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.25 Å³/Da / Density % sol: 71.06 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% PEG-3350, 0.1 M sodium citrate/citric acid, and 0.2 M sodium citrate, pH 4.0, 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: 3.05→42.9 Å / Num. obs: 22454 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_sym value: 0.045 / Net I/σ(I): 24.8

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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:

SAD / Resolution: 3.062→42.886 Å / SU ML: 0.29 / σ(F): 0.12 / Phase error: 20.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1781	950	5.02 %	Random
R_work	0.1316	-	-	-
obs	0.1339	18909	77.32 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.062→42.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2916	1734	0	0	4650

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4892
X-RAY DIFFRACTION	f_angle_d	1.452	6949
X-RAY DIFFRACTION	f_dihedral_angle_d	25.507	1961
X-RAY DIFFRACTION	f_chiral_restr	0.064	816
X-RAY DIFFRACTION	f_plane_restr	0.007	593

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 (%)
3.0622-3.2236	0.231	88	0.1485	1481	X-RAY DIFFRACTION	45
3.2236-3.4255	0.1812	109	0.1407	1850	X-RAY DIFFRACTION	55
3.4255-3.6898	0.2087	97	0.1522	2162	X-RAY DIFFRACTION	65
3.6898-4.0609	0.2186	132	0.1483	2652	X-RAY DIFFRACTION	80
4.0609-4.6479	0.1706	167	0.1263	3232	X-RAY DIFFRACTION	97
4.6479-5.8535	0.1915	184	0.144	3275	X-RAY DIFFRACTION	99
5.8535-42.8902	0.1558	173	0.1172	3307	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	2.9802	-3.5536	4.9412	8.6721	-6.1188	8.1591	-1.5265	-2.2273	2.8104	2.1294	0.0981	-1.503	-1.0009	-1.3561	1.2176	1.4541	0.1764	-0.14	1.1384	-0.1642	1.068	92.7496	58.7391	25.7692
2	7.3105	-6.472	1.1394	7.3722	0.1607	4.0452	0.558	0.6623	1.4368	-0.1467	0.1213	-0.2953	-1.1017	-0.1106	-0.3508	0.985	0.1558	0.285	0.6469	0.1801	0.9974	75.4032	69.7387	10.6284
3	3.1791	-0.2672	0.855	1.7837	0.922	7.0122	0.2665	1.4337	1.9741	-0.783	-1.1507	-0.9618	-1.1531	-0.5635	-1.4203	1.3139	0.0005	0.4791	0.3049	0.6842	1.537	74.8972	78.4385	11.4424
4	5.7504	-2.4654	1.598	7.2165	-3.0133	3.6836	-0.3086	2.5213	2.0587	-1.7028	1.0785	-0.9107	-1.4928	1.7459	-1.2229	0.7925	-0.0623	0.3123	0.9914	0.1297	1.4922	91.3491	64.0172	7.0259
5	6.6047	-4.3626	3.8027	5.1445	-5.9672	6.945	1.1218	1.454	0.1034	-2.7859	-1.5253	-0.3918	3.2605	-0.1571	0.4241	1.1543	0.0789	0.0501	0.9584	-0.1572	0.7812	79.991	57.3715	3.3545
6	3.6489	-3.7712	0.7276	8.5182	1.376	6.6276	0.0659	-0.1149	-0.4405	-0.0103	0.1278	-0.7761	0.1865	0.4772	-0.0693	0.6297	0.0497	0.1256	0.5548	-0.043	0.8933	95.5422	43.9407	20.2452
7	4.3043	-3.4234	-3.2483	2.9841	2.6582	2.8458	-0.3703	0.1232	1.3252	-0.534	1.4242	-1.6644	-0.776	2.6864	-1.3681	0.8185	0.127	0.163	1.1169	-0.0277	1.0632	97.4564	60.2213	13.8357
8	3.84	-3.3926	4.7532	3.1538	-4.1822	5.4729	-0.2506	1.71	1.7206	-1.478	-0.2067	-1.2273	0.7354	1.4909	0.5029	1.0551	-0.0701	0.1084	1.3493	0.1311	1.3455	120.0601	43.123	-3.1551
9	2.1522	3.0586	1.3591	5.8633	1.5111	3.1003	-0.698	-0.1001	1.8362	1.1419	1.3914	-2.157	-0.1538	1.012	-0.3044	0.6767	0.2779	-0.0482	1.5622	-0.5718	1.8171	131.8599	32.7723	14.6407
10	9.8669	-3.0658	0.5654	1.2495	0.9054	5.8616	-0.4348	-2.3197	-0.1862	1.2495	1.1995	-2.1131	0.4655	0.5805	-0.3775	0.7621	0.1947	-0.2313	1.9305	-0.4521	1.7964	140.616	27.3123	17.3849
11	3.2468	1.9152	-2.4542	5.7277	2.2811	4.9422	-0.2288	1.1552	-0.6598	0.0683	0.7838	-0.0095	0.267	0.5802	-0.3917	0.6299	0.0849	-0.0303	1.7988	-0.4713	1.3284	137.4092	27.5434	6.4254
12	1.548	-1.886	-0.4404	2.4755	-0.4675	3.3505	-0.5222	0.4526	2.1572	0.4819	0.3479	-1.0405	0.7304	1.4877	-0.3784	0.7656	-0.1126	0.1773	1.7208	-0.6175	1.8384	144.9784	35.2544	9.8734
13	3.0942	0.1771	-1.6934	5.5512	-5.2058	5.6436	-0.0634	-1.2317	0.6091	2.0435	0.3529	0.4692	-2.7556	1.2433	-0.1996	1.1365	0.0186	-0.1287	1.4085	-0.3273	1.5359	125.8143	41.7885	17.0406
14	4.7452	-5.3389	6.5091	6.8297	-6.304	9.3259	-1.2574	-3.043	-0.4363	0.7265	0.8526	-0.0703	0.4762	-1.9714	1.0128	0.9895	0.2343	0.1283	1.6089	-0.0207	1.0792	125.2874	28.718	19.5784
15	1.5884	-3.654	-0.4816	8.3863	1.8127	6.4145	-0.5401	-0.6183	-0.2683	-0.4468	-0.9884	-0.5739	-1.8739	0.3852	-0.0498	0.5487	-0.1019	0.0707	0.9604	-0.4927	1.072	113.5799	40.5738	2.8951
16	9.2921	0.3326	3.4586	6.1634	0.4256	5.1511	0.1097	1.2409	1.7012	-1.1279	0.2485	-0.0096	-0.8338	0.3171	0.0989	0.6081	-0.1088	0.0462	1.1388	0.0554	1.0234	104.9317	41.2549	-2.9875
17	4.4637	-1.1471	2.3734	3.5856	1.1527	4.0348	0.0525	0.3766	-0.8601	-0.1502	0.6352	-0.189	0.0499	-0.1785	-0.3712	0.5737	-0.069	0.0525	0.8214	-0.0905	1.2029	107.5712	31.0104	1.8054
18	5.8905	-1.994	2.0194	6.3947	-0.7522	3.2287	-0.0392	-0.7113	0.8325	-1.0732	0.4183	1.2348	-0.4854	-0.5584	0.0364	0.5375	0.0054	0.5226	0.8177	-0.2339	0.9798	100.357	38.2317	7.2514
19	4.2822	2.3328	-4.483	8.7529	-5.9424	6.3239	1.2227	-0.9285	0.2988	1.3258	-0.0408	0.1255	-3.2157	1.018	-1.2137	0.9938	0.0037	0.0107	1.4302	-0.5579	1.3354	119.728	46.3688	10.3971
20	4.2612	-2.5586	3.7893	2.3339	-1.9231	3.5692	-0.2804	0.7432	1.6951	-0.8644	-0.464	-1.6811	-2.6558	-0.5663	0.8524	1.6698	0.3096	-0.0789	0.7347	0.0227	1.2455	64.1012	68.7004	20.5939
21	1.3493	0.0334	-1.5335	2.0501	1.4175	1.8885	-0.8527	-0.4305	-1.4352	0.97	0.5594	0.7412	0.4481	-0.0042	0.3694	1.1035	0.3014	0.3277	0.8976	0.1772	1.3186	80.0379	38.4209	24.6093
22	9.1961	4.0452	1.0367	1.8761	-0.3248	3.591	-0.0327	-0.2474	-0.6971	1.4269	0.2662	0.6373	0.5891	0.0497	-0.1045	1.2228	0.3043	0.2775	0.8321	0.1039	1.4947	88.1113	30.5861	27.0984
23	3.5524	0.4337	-2.8221	1.3318	1.6071	4.705	-1.1059	-0.6938	-0.5238	0.3734	0.4247	0.1363	0.1809	-0.4121	0.7504	1.041	0.2325	0.1574	0.7579	0.0685	0.9935	66.2294	55.5442	21.4238
24	7.6025	4.25	3.8844	5.3393	-2.2306	8.6996	-0.552	0.6122	0.401	-0.3106	0.9346	-0.4991	-0.3168	0.7063	-0.3157	0.5178	-0.02	0.0873	1.0247	-0.1043	1.3214	110.9948	21.9789	-4.7325
25	5.0233	-6.1264	-2.6207	7.8453	1.5543	6.2829	-0.6622	1.0391	-1.5118	-0.467	0.7198	0.3985	0.8701	1.6656	0.1279	0.6979	0.1358	-0.0016	1.5053	-0.2387	1.7509	132.5746	18.041	5.1051
26	7.8318	-6.6782	3.438	6.7925	-2.88	1.3864	-0.41	0.0981	0.8066	-0.5862	-0.1922	0.8074	0.1731	0.8127	0.4006	0.8368	0.1889	0.2533	2.3795	-0.6495	1.9305	151.8282	20.236	2.0139
27	6.7726	-6.5588	-3.0218	6.4882	3.5488	4.3952	-2.362	-1.0644	-1.0374	0.9562	1.6095	1.718	1.5541	-0.2919	0.6737	1.0056	0.1923	-0.0491	2.2171	-0.5822	1.7956	154.6781	19.1369	8.858
28	2.6897	-2.3834	1.3904	2.1401	-1.2888	0.6756	0.4097	0.5306	-2.4497	0.1007	0.3224	-0.3135	0.1269	1.3225	-0.5582	0.7645	0.0621	0.0068	1.81	-0.648	1.779	131.5449	17.6706	0.1655
29	5.7185	-0.2966	-0.7408	5.2142	-0.9352	7.8783	-0.4216	0.0951	-0.8713	-0.1301	0.8732	0.5038	0.0882	-0.9123	-0.4271	0.6163	0.0282	0.231	1.5232	-0.2173	1.2625	109.4365	25.1335	-8.9237
30	5.723	3.2213	7.2701	5.9093	2.3012	2.0009	-0.0935	2.3931	-0.1643	-2.6369	3.3412	-0.123	-1.7305	-2.0539	-3.0227	1.5895	-0.0903	0.6515	1.4719	0.1586	1.2739	98.3682	18.263	-18.0969

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 77 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 87 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 88 through 102 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 25 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 26 through 87 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 88 through 102 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 6 through 25 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 26 through 40 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 41 through 55 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 56 through 68 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 69 through 87 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 88 through 102 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 6 through 25 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 26 through 40 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 41 through 55 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 56 through 68 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 69 through 87 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 88 through 102 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 1 through 5 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 6 through 22 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 2 through 11 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 12 through 22 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 1 through 10 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 11 through 15 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 16 through 22 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 2 through 6 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 7 through 16 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 17 through 21 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 22 through 22 )

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