PDB-7ne9: A single sensor controls large variations in zinc quotas in a mar...

ID or keywords:

Entry

Database: PDB / ID: 7ne9

Title

A single sensor controls large variations in zinc quotas in a marine cyanobacterium

Components

Ferric uptake regulator family

Keywords

METAL BINDING PROTEIN / zinc sensor ZUR / metallothionein activation / Marine cyanobacteria / zinc for CO2 fixation

Function / homology

Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator /

Ferric uptake regulator family / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily /

ACETATE ION /

Ferric uptake regulator family

Function and homology information

Biological species

Synechococcus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Fulop, V.

Funding support

United Kingdom, 2items

Citation

Journal: Nat.Chem.Biol. / Year: 2022
Title: A single sensor controls large variations in zinc quotas in a marine cyanobacterium.
Authors: Mikhaylina, A. / Ksibe, A.Z. / Wilkinson, R.C. / Smith, D. / Marks, E. / Coverdale, J.P.C. / Fulop, V. / Scanlan, D.J. / Blindauer, C.A.

History

Deposition	Feb 3, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 22, 2022	Group: Database references / Derived calculations / Category: atom_type / citation / citation_author Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 10, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ne9.cif.gz	186 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/7ne9 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7ne9	HTTPS FTP

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Related structure data

Similar structure data	5lsw-d 7ccx-d 3ecr-d 3rw6-1 4k5b-d 6y5p-d 4ief-4 1tnu-4 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

AAA: Ferric uptake regulator family

BBB: Ferric uptake regulator family

CCC: Ferric uptake regulator family

DDD: Ferric uptake regulator family

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	129.250, 129.250, 77.280
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	1	Chains AAA CCC
3	1	Chains AAA DDD
4	1	Chains BBB CCC
5	1	Chains BBB DDD
6	1	Chains CCC DDD

#1: Protein	Ferric uptake regulator family / Mass: 14855.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (strain WH8102) (bacteria) Strain: WH8102 / Gene: SYNW2401 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7U3N0
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.14 Å³/Da / Density % sol: 60.78 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: 100 mM magnesium acetate, 100 mM MES pH 6, 16% (w/v) PEG 10000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2827 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2827 Å / Relative weight: 1
Reflection	Resolution: 2.1→77.3 Å / Num. obs: 43002 / % possible obs: 99.9 % / Redundancy: 39.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.193 / Net I/σ(I): 19.4
Reflection shell	Resolution: 2.1→2.21 Å / Num. unique obs: 30185 / CC_1/2: 0.754 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→64.625 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.953 / SU B: 8.865 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2178	1654	3.846 %
R_work	0.1944	41348	-
all	0.195	-	-
obs	-	43002	99.998 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 47.106 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.359 Å²	0.179 Å²	0 Å²
2-	-	0.359 Å²	0 Å²
3-	-	-	-1.164 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→64.625 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3712	0	13	140	3865

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	3826
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3427
X-RAY DIFFRACTION	r_angle_refined_deg	1.608	1.654	5160
X-RAY DIFFRACTION	r_angle_other_deg	1.373	1.579	7893
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.521	5	470
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.608	20.847	236
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.19	15	604
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	26.697	15	20
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.274	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	478
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4325
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	839
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	710
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	2883
X-RAY DIFFRACTION	r_nbtor_refined	0.154	0.2	1794
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.109	0.2	1737
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	85
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.212	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.166	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.205	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.184	3.338	1905
X-RAY DIFFRACTION	r_mcbond_other	2.167	3.334	1903
X-RAY DIFFRACTION	r_mcangle_it	3.681	4.963	2366
X-RAY DIFFRACTION	r_mcangle_other	3.681	4.965	2367
X-RAY DIFFRACTION	r_scbond_it	3.069	3.661	1919
X-RAY DIFFRACTION	r_scbond_other	3.069	3.662	1920
X-RAY DIFFRACTION	r_scangle_it	4.377	5.396	2794
X-RAY DIFFRACTION	r_scangle_other	4.377	5.397	2795
X-RAY DIFFRACTION	r_lrange_it	6.779	38.827	3937
X-RAY DIFFRACTION	r_lrange_other	6.777	38.772	3929
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.125	0.05	3248
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.119	0.05	3197
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.131	0.05	3200
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.125	0.05	3244
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.101	0.05	3293
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.133	0.05	3148

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	WR_factor R_work
2.1-2.154	0.321	154	0.282	3031	0.284	3185	0.781	0.802	0.26
2.154-2.213	0.318	121	0.264	2959	0.266	3080	0.826	0.846	0.238
2.213-2.278	0.264	105	0.247	2861	0.247	2966	0.881	0.867	0.215
2.278-2.348	0.292	109	0.233	2828	0.235	2937	0.855	0.888	0.201
2.348-2.424	0.309	99	0.228	2699	0.231	2798	0.863	0.896	0.191
2.424-2.509	0.25	112	0.21	2617	0.212	2729	0.912	0.927	0.174
2.509-2.604	0.229	91	0.193	2538	0.195	2629	0.92	0.942	0.16
2.604-2.71	0.277	85	0.214	2466	0.216	2551	0.921	0.934	0.18
2.71-2.83	0.238	84	0.221	2359	0.222	2443	0.929	0.928	0.19
2.83-2.968	0.242	107	0.212	2226	0.213	2333	0.92	0.932	0.184
2.968-3.128	0.248	82	0.204	2148	0.205	2230	0.931	0.94	0.181
3.128-3.318	0.248	88	0.199	2011	0.201	2099	0.929	0.945	0.182
3.318-3.546	0.222	74	0.19	1891	0.191	1965	0.94	0.954	0.181
3.546-3.829	0.204	48	0.182	1795	0.183	1843	0.95	0.96	0.177
3.829-4.193	0.197	66	0.166	1643	0.167	1709	0.957	0.967	0.165
4.193-4.686	0.15	67	0.147	1479	0.147	1546	0.976	0.975	0.152
4.686-5.406	0.16	65	0.171	1303	0.171	1368	0.977	0.973	0.176
5.406-6.609	0.209	51	0.2	1101	0.2	1152	0.957	0.956	0.201
6.609-9.299	0.199	38	0.175	875	0.176	913	0.955	0.962	0.193
9.299-64.625	0.107	8	0.19	517	0.189	525	0.978	0.968	0.218

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	1.1324	0.9555	0.3034	2.9224	0.5028	4.353	0.004	0.0162	0.0204	-0.02	0.0046	0.0162	0.0639	-0.3834	-0.0086	0.114	0.0144	0.0053	0.1743	0.0103	0.0011	12.39	58.671	28.176
2	1.236	-0.4569	0.3107	2.8294	-0.0104	0.6901	-0.0193	0.0912	-0.0762	0.1009	-0.0546	-0.3112	0.0801	0.021	0.0739	0.1582	0.0728	-0.023	0.1725	-0.0107	0.0716	23.438	69.141	42.144
3	0.7594	-0.5066	-0.2768	3.7348	-2.2001	2.0683	-0.027	0.0112	0.0673	0.048	-0.0576	-0.0711	-0.0308	0.0205	0.0846	0.2061	0.0378	-0.0449	0.1087	0.0379	0.0622	17.531	89.827	32.418
4	2.3821	0.9512	-1.1396	1.7956	-0.2717	2.3996	-0.0418	0.1911	-0.0082	0.3179	0.0543	0.0171	-0.2048	-0.1643	-0.0125	0.2164	0.0876	-0.0151	0.1424	0.0057	0.0199	15.608	74.09	46.135
5	3.6241	-0.1077	-1.7198	0.1209	0.3165	3.0279	-0.3049	-0.0562	-0.2986	0.0957	0.0144	0.1529	0.1313	0.0807	0.2904	0.1523	0.0635	0.1614	0.1794	0.0122	0.2243	20.703	38.647	42.375
6	0.9796	-0.5923	-0.3197	3.3319	-0.4115	1.1631	-0.1389	0.1684	-0.1601	-0.1597	-0.0076	0.2787	-0.0079	-0.1374	0.1465	0.153	0.04	0.0375	0.2256	-0.0196	0.0767	32.428	44.617	26.649
7	2.2509	1.0357	1.5616	1.2313	0.6714	3.9036	-0.044	0.092	-0.0821	0.0551	-0.048	-0.0615	-0.3424	0.1269	0.0921	0.1929	0.0158	0.0095	0.1832	-0.0031	0.0169	46.566	54.656	42.964
8	2.6237	-1.3791	-1.2298	3.1394	-0.4759	1.6844	-0.1167	-0.1032	-0.2511	0.068	0.067	0.1924	0.057	0.1647	0.0498	0.1413	0.0664	0.0281	0.2105	-0.0265	0.0388	40.486	39.656	29.922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	6 - 73
2	X-RAY DIFFRACTION	2	ALL	AAA	74 - 128
3	X-RAY DIFFRACTION	3	ALL	BBB	6 - 73
4	X-RAY DIFFRACTION	4	ALL	BBB	74 - 128
5	X-RAY DIFFRACTION	5	ALL	CCC	6 - 73
6	X-RAY DIFFRACTION	6	ALL	CCC	74 - 128
7	X-RAY DIFFRACTION	7	ALL	DDD	6 - 73
8	X-RAY DIFFRACTION	8	ALL	DDD	74 - 128

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