PDB-2y3g: Se-Met form of Cupriavidus metallidurans CH34 CnrXs

ID or keywords:

Entry

Database: PDB / ID: 2y3g

Title

Se-Met form of Cupriavidus metallidurans CH34 CnrXs

Components

NICKEL AND COBALT RESISTANCE PROTEIN CNRR

Keywords

METAL BINDING PROTEIN

Function / homology

Heavy-metal resistance protein / Heavy-metal resistance / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / periplasmic space / Up-down Bundle / Mainly Alpha / Nickel and cobalt resistance protein CnrR

Function and homology information

Biological species

CUPRIAVIDUS METALLIDURANS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.91 Å

Authors

Trepreau, J. / Girard, E. / Maillard, A.P. / de Rosny, E. / Petit-Haertlein, I. / Kahn, R. / Coves, J.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for Metal Sensing by Cnrx.
Authors: Trepreau, J. / Girard, E. / Maillard, A.P. / De Rosny, E. / Petit-Haertlein, I. / Kahn, R. / Coves, J.

History

Deposition	Dec 20, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y3g.cif.gz	195.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2y3g.ent.gz	167.5 KB	Display	PDB format
PDBx/mmJSON format	2y3g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2y3g_validation.pdf.gz	462.7 KB	Display	wwPDB validaton report
Full document	2y3g_full_validation.pdf.gz	469.6 KB	Display
Data in XML	2y3g_validation.xml.gz	21.4 KB	Display
Data in CIF	2y3g_validation.cif.gz	30.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y3/2y3g ftp://data.pdbj.org/pub/pdb/validation_reports/y3/2y3g	HTTPS FTP

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Related structure data

Related structure data	2y39C 2y3bC 2y3dC 2y3hC C: citing same article (ref.)
Similar structure data	2y3h-2 3epv-2 1zko-3 3epv-1 3zg1-2 3zg1-1 1ynm-d 4cv4-1 2y3b-1 3e5s-d 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

Deposited unit

A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

B: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

C: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

D: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

hetero molecules

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

1

A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

D: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

hetero molecules

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

2

B: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

C: NICKEL AND COBALT RESISTANCE PROTEIN CNRR

hetero molecules

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

Unit cell

Length a, b, c (Å)	31.896, 81.809, 93.336
Angle α, β, γ (deg.)	90.00, 90.47, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	NICKEL AND COBALT RESISTANCE PROTEIN CNRR / NICKEL AND COBALT RESISTANCE PROTEIN CNRX Mass: 13358.770 Da / Num. of mol.: 4 / Fragment: METAL-SENSOR DOMAIN, RESIDUES 31-148 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: CH34 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37975
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.28 Å³/Da / Density % sol: 35 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 16% PEG 2000MME, 15% GLYCEROL., pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9795
Detector	Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2009
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.91→46.67 Å / Num. obs: 36868 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / B_iso Wilson estimate: 26.79 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.91→2.01 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.23 / Mean I/σ(I) obs: 3.3 / % possible all: 95.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.91→46.666 Å / SU ML: 0.27 / σ(F): 1.39 / Phase error: 26.01 / Stereochemistry target values: ML
Details: RESIDUES 31-39 ARE DISORDERED. RESIDUES 1-30 ARE NOT PRESENT IN THE CONSTRUCT.

	R_factor	Num. reflection	% reflection
R_free	0.2382	1848	5 %
R_work	0.1873	-	-
obs	0.1899	36813	98.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 61.144 Å² / k_sol: 0.372 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.9091 Å²	0 Å²	-0.9882 Å²
2-	-	20.8333 Å²	0 Å²
3-	-	-	-11.9242 Å²

Refinement step

Cycle: LAST / Resolution: 1.91→46.666 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3479	0	24	264	3767

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3706
X-RAY DIFFRACTION	f_angle_d	0.893	5014
X-RAY DIFFRACTION	f_dihedral_angle_d	14.926	1460
X-RAY DIFFRACTION	f_chiral_restr	0.06	539
X-RAY DIFFRACTION	f_plane_restr	0.004	688

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 (%)
1.9101-1.9617	0.3076	135	0.2355	2529	X-RAY DIFFRACTION	95
1.9617-2.0195	0.2755	143	0.2005	2671	X-RAY DIFFRACTION	98
2.0195-2.0847	0.2984	143	0.1915	2678	X-RAY DIFFRACTION	99
2.0847-2.1592	0.2315	143	0.1815	2686	X-RAY DIFFRACTION	99
2.1592-2.2456	0.2468	146	0.1726	2707	X-RAY DIFFRACTION	99
2.2456-2.3478	0.257	137	0.181	2666	X-RAY DIFFRACTION	99
2.3478-2.4716	0.2695	148	0.1957	2722	X-RAY DIFFRACTION	99
2.4716-2.6264	0.2709	142	0.1962	2678	X-RAY DIFFRACTION	99
2.6264-2.8292	0.2788	139	0.1899	2703	X-RAY DIFFRACTION	99
2.8292-3.1138	0.2614	146	0.1993	2705	X-RAY DIFFRACTION	100
3.1138-3.5643	0.2068	145	0.1865	2746	X-RAY DIFFRACTION	100
3.5643-4.4901	0.2055	144	0.1627	2722	X-RAY DIFFRACTION	100
4.4901-46.6804	0.2191	137	0.1985	2752	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	1.1481	-0.16	-1.5413	5.9835	-3.1881	6.5837	0.6474	0.6784	-0.2019	0.4802	0.6475	2.5999	0.5362	-1.2524	-0.9069	0.3095	0.0045	0.0831	0.5545	-0.0329	0.7888	12.3095	18.0874	68.2526
2	0.3675	0.494	0.186	0.6146	-0.2898	0.5392	0.0314	-0.1219	0.2318	-0.141	-0.0854	0.2472	0.0918	-0.4359	0.1096	0.1911	0.0047	-0.017	0.1771	-0.019	0.2661	8.9057	10.2363	59.5504
3	0.4552	0.2095	-0.3199	0.4079	-0.8847	3.4097	-0.1499	-0.1303	-0.1598	-0.1626	0.0205	0.0014	0.7103	-0.9765	0.1038	0.2487	-0.0271	0.0012	0.3312	0.008	0.2305	12.3492	-0.1726	86.7684
4	0.4559	0.5121	0.0118	1.1404	-0.7657	1.405	0.082	-0.2445	-0.3311	-0.2134	0.1118	-0.0479	0.723	0.1104	-0.2097	0.2975	0.0055	0.001	0.2211	0.0279	0.2808	21.2617	-2.1847	92.9391
5	0.5622	0.2206	0.3617	0.3303	-0.0044	0.6788	-0.0475	-0.1417	0.273	-0.1318	-0.029	-0.2301	0.1792	-0.1376	0.0452	0.2177	-0.0108	0.0034	0.1593	-0.0381	0.2358	20.2889	6.6726	72.6633
6	1.0006	-0.2023	0.5157	0.6196	-0.7777	0.9672	-0.3009	0.1051	0.4413	0.0401	-0.0105	0.1435	-0.4292	0.1097	0.2022	0.1951	-0.0187	-0.0411	0.0127	0.0279	0.1749	20.6278	19.261	62.2873
7	0.3393	1.0164	0.058	3.8201	-0.7597	1.1092	0.3346	-0.4932	-0.4291	0.1399	-0.2456	-1.802	0.1026	0.2607	0.1259	0.2993	0.0733	-0.0709	0.3134	0.2019	0.4883	34.5511	32.965	41.8694
8	0.139	-0.2108	0.0842	0.7947	-0.4092	0.8322	0.0243	-0.0793	-0.5705	-0.3177	0.0828	-0.4912	0.3121	0.1826	-0.1064	0.2642	0.0189	0.0469	0.1941	-0.0157	0.3733	39.1501	39.2348	30.0177
9	0.1945	-0.2365	-0.6629	0.2508	1.0236	5.9072	0.2048	-0.1638	0.0636	-0.0732	0.2564	-0.2038	-0.2212	1.1845	-0.0503	0.2161	-0.0237	0.0029	0.3585	0.0095	0.2626	36.0862	49.4006	49.3971
10	0.4759	-0.0873	0.1521	0.6521	0.1439	0.7142	-0.0352	-0.0191	0.2969	0.0883	0.02	0.0323	-0.0093	0.2917	-0.0481	0.2755	-0.0638	-0.0012	0.3049	-0.0203	0.2426	29.163	54.4952	68.6312
11	0.6797	0.0811	-0.6215	0.4658	0.5748	1.8801	-0.0231	-0.0681	-0.0134	-0.0489	-0.0897	0.117	-0.0166	0.4714	0.1752	0.101	-0.0026	-0.014	0.0925	0.0289	0.1236	27.7758	43.4848	44.1427
12	1.4631	0.6198	-0.5798	0.4322	0.5354	1.6116	-0.254	0.2418	-0.847	-0.1628	-0.146	-0.473	0.8585	-0.2882	0.1763	0.3487	-0.0472	0.0409	0.1899	0.0045	0.352	25.8392	30.6869	36.4276
13	3.7882	-1.3084	0.7777	1.5964	0.0157	2.0768	0.0291	0.4759	-1.3327	0.1609	0.4181	0.7694	0.5345	0.1083	-0.4331	0.5154	0.0134	0.0009	0.5506	-0.0191	0.5614	33.6487	35.9405	72.2716
14	0.331	0.0368	0.3047	0.1709	-0.112	0.4916	-0.4057	-0.0121	0.0487	0.0352	0.2206	0.2777	0.5878	0.1901	0.0966	0.4906	0.0337	0.006	0.5954	0.0801	0.2915	24.8357	33.2475	82.887
15	0.7329	0.0765	1.217	0.1914	0.6816	4.7321	0.0782	-0.4461	0.1128	0.0358	-0.0442	-0.046	1.5481	-1.2772	-0.0489	0.4111	-0.1637	-0.0139	0.4554	0.0363	0.2425	19.0389	34.7176	64.6923
16	0.2839	-0.4102	-0.2625	0.4483	0.6217	1.6721	0.1375	-0.0035	0.0482	0.1001	-0.2273	-0.038	0.2872	-0.8515	0.0161	0.2382	-0.0957	-0.0346	0.2758	0.0316	0.202	16.6351	37.525	42.467
17	0.8842	-0.1454	1.1001	0.2933	0.5107	2.5058	0.0409	-0.3971	0.1781	-0.0021	-0.1975	-0.0498	0.3365	-0.795	0.0955	0.1573	-0.0542	0.006	0.263	0.0061	0.1808	23.5627	43.105	67.9279
18	0.2577	0.2975	-0.026	0.4161	-0.4924	0.8437	0.009	0.1184	0.0551	-0.088	-0.2336	-0.1836	0.0208	0.9093	0.1416	0.175	0.0189	-0.0008	0.4801	0.0318	0.1918	36.9778	45.3567	75.6195
19	1.7253	0.7533	-1.4164	0.3701	-0.3252	3.3116	0.6169	0.2716	1.1844	-0.126	-0.171	-0.2298	-0.5529	0.7328	-0.169	0.3547	-0.0578	-0.0183	0.4914	0.1958	0.7387	12.4997	16.5979	96.3465
20	1.166	0.8473	-0.9864	0.7293	-0.873	2.902	0.0747	0.0089	-0.6532	-0.5045	-0.2615	-0.3927	-1.5877	0.2978	0.1356	0.5893	0.0132	0.0524	0.6836	-0.1924	0.4575	18.9038	19.4838	108.3361
21	0.7253	-0.044	-1.3833	0.2286	0.0703	2.6084	0.1325	-0.4913	-0.0018	0.2928	0.1678	0.5439	-0.9582	1.2611	-0.1985	0.6749	-0.2732	0.1073	0.527	-0.0166	0.2964	27.4445	17.895	91.0219
22	0.1904	-0.0252	0.3738	0.7523	0.1999	1.1534	0.1253	-0.0432	-0.1061	0.238	-0.1044	-0.451	0.1719	0.5432	0.0836	0.2407	-0.096	0.0037	0.2241	-0.0115	0.2073	29.8414	16.0151	68.2312
23	0.8409	-0.2403	-1.4674	-0.0006	0.2466	5.0178	-0.0244	-0.2109	0.3624	-0.0057	0.1798	-0.0336	0.38	0.8362	-0.162	0.2389	-0.0301	0.0041	0.3079	-0.0196	0.2382	28.5387	8.8341	77.2192
24	0.6753	0.1256	-1.0394	0.4113	-0.2854	1.1831	0.0158	0.0251	0.0827	-0.0123	0.0996	0.0496	-0.206	-0.2878	-0.0626	0.1716	0.0428	0.0173	0.3705	-0.0127	0.2531	14.5518	8.2695	101.0272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 40:48)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 49:68)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 69:92)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 93:105)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 106:122)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 123:148)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 39:49)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 50:62)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 63:79)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 80:105)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 106:125)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 126:148)
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 40:50)
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESID 51:62)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 63:77)
16	X-RAY DIFFRACTION	16	(CHAIN C AND RESID 78:103)
17	X-RAY DIFFRACTION	17	(CHAIN C AND RESID 104:127)
18	X-RAY DIFFRACTION	18	(CHAIN C AND RESID 128:148)
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 40:48)
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 49:62)
21	X-RAY DIFFRACTION	21	(CHAIN D AND RESID 63:76)
22	X-RAY DIFFRACTION	22	(CHAIN D AND RESID 77:95)
23	X-RAY DIFFRACTION	23	(CHAIN D AND RESID 96:113)
24	X-RAY DIFFRACTION	24	(CHAIN D AND RESID 114:148)

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