PDB-5dy1: Crystal of Selenomethionine substituted AmtR from Corynebacterium...

ID or keywords:

Entry

Database: PDB / ID: 5dy1

Title

Crystal of Selenomethionine substituted AmtR from Corynebacterium glutamicum

Components

TetR family transcriptional regulator

Keywords

DNA BINDING PROTEIN / TetR family regulator / Nitrogen master regulator / PII / GlnK / GlnB / TFR

Function / homology

Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / metal ion binding / TetR family transcriptional regulator

Function and homology information

Biological species

Corynebacterium glutamicum ATCC 14067 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.651 Å

Authors

Palanca, C. / Rubio, V.

Funding support

Spain, 1items

Citation

Journal: Febs J. / Year: 2016
Title: Structure of AmtR, the global nitrogen regulator of Corynebacterium glutamicum, in free and DNA-bound forms.
Authors: Palanca, C. / Rubio, V.

History

Deposition	Sep 24, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 20, 2016	Group: Database references
Revision 1.2	Mar 30, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5dy1.cif.gz	166 KB	Display	PDBx/mmCIF format
PDB format	pdb5dy1.ent.gz	140 KB	Display	PDB format
PDBx/mmJSON format	5dy1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5dy1_validation.pdf.gz	431.6 KB	Display	wwPDB validaton report
Full document	5dy1_full_validation.pdf.gz	434.1 KB	Display
Data in XML	5dy1_validation.xml.gz	15.4 KB	Display
Data in CIF	5dy1_validation.cif.gz	20.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dy/5dy1 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/5dy1	HTTPS FTP

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Related structure data

Related structure data	5dxzC 5dy0C C: citing same article (ref.)
Similar structure data	5mqq-3 5mqq-2 5mqq-1 5dxz-1 3vpr-1 4d5f-1 3vpr-2 5fgl-1 3btl-1 3bti-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

Deposited unit

A: TetR family transcriptional regulator

B: TetR family transcriptional regulator

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	160.464, 160.464, 52.435
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	23 - 220
2	0	1	0	B	23 - 220

#1: Protein	TetR family transcriptional regulator Mass: 24641.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Selnomethionine derivative Source: (gene. exp.) Corynebacterium glutamicum ATCC 14067 (bacteria) Gene: KIQ_008455 / Plasmid: pLIC-SGC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072Z681
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.64 Å³/Da / Density % sol: 53.45 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Na/K phosphate pH 7, 0.2 M NaCl, 6% PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.981 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2012

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9791	1
2	0.981	1

Reflection

Resolution: 2.651→80.232 Å / Num. all: 14116 / Num. obs: 14116 / % possible obs: 96.4 % / Redundancy: 3.4 % / R_pim(I) all: 0.061 / R_rim(I) all: 0.116 / R_sym value: 0.076 / Net I/av σ(I): 6 / Net I/σ(I): 10.4 / Num. measured all: 47544

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2.65-2.79	2.3	0.339	2.3	4134	1790	0.301	0.339	2.1	82.8
2.79-2.96	3.2	0.277	2.7	6151	1947	0.214	0.277	3.4	96
2.96-3.17	3.6	0.213	3.5	6838	1881	0.152	0.213	5	99.6
3.17-3.42	3.5	0.138	5.3	6169	1774	0.103	0.138	7.2	99.5
3.42-3.75	3.7	0.1	7.2	5988	1633	0.073	0.1	10.1	99.7
3.75-4.19	3.6	0.068	10.5	5092	1430	0.052	0.068	14.4	99.2
4.19-4.84	3.6	0.052	13.3	4671	1282	0.04	0.052	18.5	99
4.84-5.93	3.5	0.055	13	3863	1090	0.048	0.055	16.9	99.1
5.93-8.38	3.6	0.041	16.4	3023	840	0.038	0.041	20.9	99.1
8.38-49.059	3.6	0.023	27.9	1615	449	0.023	0.023	37.6	97.6

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
SCALA	3.3.20	data scaling
PDB_EXTRACT	3.15	data extraction
PHENIX		phasing
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.651→49.11 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.923 / WR_factor R_free: 0.2012 / WR_factor R_work: 0.1656 / FOM work R set: 0.7996 / SU B: 27.747 / SU ML: 0.241 / SU R Cruickshank DPI: 0.9157 / SU R_free: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.916 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2208	719	5.1 %	RANDOM
R_work	0.1805	-	-	-
obs	0.1826	13397	96.38 %	-

Solvent computation

Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK

Displacement parameters

B_iso max: 163.61 Å² / B_iso mean: 53.166 Å² / B_iso min: 19.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.23 Å²	0.23 Å²	-0 Å²
2-	-	0.23 Å²	0 Å²
3-	-	-	-0.76 Å²

Refinement step

Cycle: final / Resolution: 2.651→49.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3098	0	2	10	3110
B_iso mean	-	-	45.53	33.09	-
Num. residues	-	-	-	-	403

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	3174
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3063
X-RAY DIFFRACTION	r_angle_refined_deg	1.096	1.985	4326
X-RAY DIFFRACTION	r_angle_other_deg	0.999	3	7052
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.764	5	405
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.483	23.769	130
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.064	15	507
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.724	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	518
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	3542
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	676
X-RAY DIFFRACTION	r_mcbond_it	5.11	3.216	1614
X-RAY DIFFRACTION	r_mcbond_other	5.092	3.215	1613
X-RAY DIFFRACTION	r_mcangle_it	7.279	4.836	2015

Refine LS restraints NCS

Ens-ID: 1 / Number: 27289 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.651→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.349	42	-
R_work	0.312	814	-
all	-	856	-
obs	-	-	78.24 %

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	3.5733	-2.3445	-1.1778	5.3322	0.9086	1.4286	0.217	0.0472	0.0421	-0.3581	-0.0272	0.0191	-0.0915	-0.1498	-0.1898	0.1092	0.0667	-0.0154	0.1023	-0.0007	0.0937	28.12	62.317	40.198
2	13.0962	1.4903	1.1735	0.9463	0.3719	0.1816	-0.0895	-0.2184	0.9053	-0.05	0.0529	-0.0979	-0.0306	0.026	0.0366	0.1458	-0.0973	0.0348	0.1763	0.0411	0.2111	55.225	61.821	29.8
3	6.2411	-0.676	-2.7125	1.5932	0.3864	1.1978	-0.1063	0.2422	0.493	-0.1096	0.2696	-0.0289	0.0406	-0.0821	-0.1633	0.0796	0.0038	-0.0069	0.1757	0.0294	0.1912	52.36	61.3	40.055
4	2.2009	-2.7977	0.9901	4.9398	1.1186	4.5345	-0.1459	-0.0575	0.0059	0.0797	-0.0646	0.1228	-0.2119	-0.2581	0.2105	0.1119	-0.0161	-0.0567	0.1491	0.0254	0.1078	38.976	51.602	33.432
5	3.1837	-2.0007	2.1091	1.3384	-2.0232	7.4279	0.1654	0.3015	-0.1867	-0.1219	-0.1585	0.096	0.2277	-0.0686	-0.0069	0.1356	-0.092	0.0528	0.1467	-0.0228	0.1554	58.812	49.032	31.676
6	4.4612	-0.0141	-1.0031	0.8443	0.3091	0.344	0.1505	0.0015	0.1499	0.1576	-0.0133	-0.2052	0.0018	-0.0205	-0.1371	0.1023	0.0297	0.0372	0.1316	0.0048	0.1842	49.536	62.42	47.338
7	6.8131	-6.3077	-1.0187	6.2817	2.2294	3.9694	0.0174	-0.3398	-0.1715	-0.0414	0.299	0.0255	-0.0056	0.0947	-0.3164	0.0913	0.0177	0.0339	0.132	0.0405	0.1492	62.409	55.317	43.104
8	14.0753	-9.431	2.9439	15.1838	-6.3508	2.8004	-0.3269	0.4941	0.9713	-0.3974	0.2463	-0.5779	0.2521	-0.188	0.0806	0.0845	-0.086	-0.0771	0.1102	0.0267	0.3205	64.585	67.253	37.115
9	3.6205	2.172	1.7444	8.216	2.4558	2.9531	-0.0569	0.0378	-0.0347	0.0699	-0.0428	0.239	0.2403	-0.0585	0.0996	0.0761	-0.019	0.006	0.0835	0.004	0.0951	29.675	30.684	42.814
10	2.3213	5.8484	-0.3936	15.6504	-0.6582	0.1991	0.8036	-0.6389	0.0309	1.1991	-1.3526	0.9737	-0.2065	0.145	0.549	0.4692	-0.1812	-0.179	0.1876	0.1047	1.1256	27.33	29.909	51.196
11	8.1587	1.1569	-0.0584	0.1819	0.0946	1.03	0.1696	-0.3513	-0.5857	0.0307	-0.0871	-0.0896	0.1573	-0.0013	-0.0826	0.0955	0.0467	-0.0244	0.1718	0.0044	0.1922	50.483	32.956	56.081
12	1.0825	0.9475	0.6466	0.9516	0.5183	0.4051	0.1905	-0.3067	-0.1087	0.0792	-0.1412	-0.1201	0.1357	-0.2322	-0.0493	0.1695	-0.06	-0.0258	0.2537	0.0008	0.1315	54.89	34.12	47.614
13	3.7834	-3.2527	-1.0245	2.8168	0.5214	8.7496	-0.0775	0.1795	-0.0056	0.09	-0.1839	-0.0023	-0.444	-0.1849	0.2614	0.0835	-0.0548	0.0392	0.1656	-0.0235	0.1344	38.675	42.784	52.093
14	3.9028	2.6065	-1.7996	2.1105	-0.391	2.7033	0.0127	-0.1508	0.1645	-0.0467	-0.0772	0.1746	-0.2271	0.0254	0.0644	0.1251	0.0864	-0.0511	0.1712	-0.013	0.1251	58.069	46.138	55.287
15	6.6914	0.8933	2.4267	0.7901	0.1096	0.9486	-0.1112	0.3371	0.0227	0.0492	0.0975	-0.0074	-0.0596	0.1047	0.0137	0.083	0.0137	0.0391	0.1782	-0.028	0.1215	54.388	34.21	40.419
16	5.1782	0.949	0.9313	7.7337	-1.1121	0.5449	0.1047	-0.2344	-0.5755	0.3322	0.0812	-0.6116	-0.0133	0.0378	-0.1858	0.0608	0.0489	-0.0348	0.111	-0.0692	0.2686	65.531	31.517	50.028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 71
2	X-RAY DIFFRACTION	2	A	72 - 94
3	X-RAY DIFFRACTION	3	A	95 - 115
4	X-RAY DIFFRACTION	4	A	116 - 135
5	X-RAY DIFFRACTION	5	A	136 - 163
6	X-RAY DIFFRACTION	6	A	164 - 185
7	X-RAY DIFFRACTION	7	A	186 - 202
8	X-RAY DIFFRACTION	8	A	203 - 220
9	X-RAY DIFFRACTION	9	B	20 - 55
10	X-RAY DIFFRACTION	10	B	56 - 66
11	X-RAY DIFFRACTION	11	B	67 - 91
12	X-RAY DIFFRACTION	12	B	92 - 115
13	X-RAY DIFFRACTION	13	B	116 - 134
14	X-RAY DIFFRACTION	14	B	135 - 162
15	X-RAY DIFFRACTION	15	B	163 - 197
16	X-RAY DIFFRACTION	16	B	198 - 220

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