PDB-4fc4: FNT family ion channel

ID or keywords:

Entry

Database: PDB / ID: 4fc4

Title

FNT family ion channel

Components

Nitrite transporter NirC

Keywords

TRANSPORT PROTEIN / alpha-helical inner membrane protein /

ion channel /

cytoplasmic membrane

Function / homology

Function and homology information

transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Lue, W. / Schwarzer, N. / Du, J. / Gerbig-Smentek, E. / Andrade, S.L.A. / Einsle, O.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium.
Authors: Lu, W. / Schwarzer, N.J. / Du, J. / Gerbig-Smentek, E. / Andrade, S.L. / Einsle, O.

History

Deposition	May 24, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4fc4.cif.gz	919.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fc/4fc4 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fc4	HTTPS FTP

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Related structure data

Related structure data	3q7kS S: Starting model for refinement
Similar structure data	3tds-d 3tdr-1 3te1-d 3tdr-2 3tdo-d 3tdx-d 3te2-d 3te0-d 3kcu-d 3kcv-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
Related items in Molecule of the Month	#173 - May 2014 Aquaporin similarity (1)

Deposited unit

A: Nitrite transporter NirC

B: Nitrite transporter NirC

C: Nitrite transporter NirC

D: Nitrite transporter NirC

E: Nitrite transporter NirC

F: Nitrite transporter NirC

G: Nitrite transporter NirC

H: Nitrite transporter NirC

I: Nitrite transporter NirC

J: Nitrite transporter NirC

hetero molecules

281 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nitrite transporter NirC

B: Nitrite transporter NirC

C: Nitrite transporter NirC

D: Nitrite transporter NirC

E: Nitrite transporter NirC

defined by author&software
140 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Nitrite transporter NirC

G: Nitrite transporter NirC

H: Nitrite transporter NirC

I: Nitrite transporter NirC

J: Nitrite transporter NirC

hetero molecules

defined by author&software
141 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	176.300, 101.840, 205.300
Angle α, β, γ (deg.)	90.00, 101.24, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	1	MET	MET	ALA	ALA	B	B	1 - 248	1 - 248
1	2	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	2	MET	MET	ALA	ALA	C	C	1 - 248	1 - 248
1	3	PHE	PHE	ALA	ALA	A	A	2 - 248	2 - 248
2	3	PHE	PHE	ALA	ALA	D	D	2 - 248	2 - 248
1	4	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	4	MET	MET	ALA	ALA	E	E	1 - 248	1 - 248
1	5	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	5	MET	MET	ALA	ALA	F	F	1 - 248	1 - 248
1	6	PHE	PHE	ALA	ALA	A	A	2 - 248	2 - 248
2	6	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
1	7	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	7	MET	MET	ALA	ALA	H	H	1 - 248	1 - 248
1	8	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	8	MET	MET	ALA	ALA	I	I	1 - 248	1 - 248
1	9	MET	MET	ALA	ALA	A	A	1 - 248	1 - 248
2	9	MET	MET	ALA	ALA	J	J	1 - 248	1 - 248
1	10	MET	MET	PRO	PRO	B	B	1 - 250	1 - 250
2	10	MET	MET	PRO	PRO	C	C	1 - 250	1 - 250
1	11	PHE	PHE	THR	THR	B	B	2 - 249	2 - 249
2	11	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
1	12	MET	MET	PRO	PRO	B	B	1 - 250	1 - 250
2	12	MET	MET	PRO	PRO	E	E	1 - 250	1 - 250
1	13	MET	MET	PRO	PRO	B	B	1 - 250	1 - 250
2	13	MET	MET	PRO	PRO	F	F	1 - 250	1 - 250
1	14	PHE	PHE	ALA	ALA	B	B	2 - 248	2 - 248
2	14	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
1	15	MET	MET	PRO	PRO	B	B	1 - 250	1 - 250
2	15	MET	MET	PRO	PRO	H	H	1 - 250	1 - 250
1	16	MET	MET	PRO	PRO	B	B	1 - 250	1 - 250
2	16	MET	MET	PRO	PRO	I	I	1 - 250	1 - 250
1	17	MET	MET	PRO	PRO	B	B	1 - 250	1 - 250
2	17	MET	MET	PRO	PRO	J	J	1 - 250	1 - 250
1	18	PHE	PHE	THR	THR	C	C	2 - 249	2 - 249
2	18	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
1	19	MET	MET	PRO	PRO	C	C	1 - 250	1 - 250
2	19	MET	MET	PRO	PRO	E	E	1 - 250	1 - 250
1	20	MET	MET	PRO	PRO	C	C	1 - 250	1 - 250
2	20	MET	MET	PRO	PRO	F	F	1 - 250	1 - 250
1	21	PHE	PHE	ALA	ALA	C	C	2 - 248	2 - 248
2	21	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
1	22	MET	MET	PRO	PRO	C	C	1 - 250	1 - 250
2	22	MET	MET	PRO	PRO	H	H	1 - 250	1 - 250
1	23	MET	MET	PRO	PRO	C	C	1 - 250	1 - 250
2	23	MET	MET	PRO	PRO	I	I	1 - 250	1 - 250
1	24	MET	MET	PRO	PRO	C	C	1 - 250	1 - 250
2	24	MET	MET	PRO	PRO	J	J	1 - 250	1 - 250
1	25	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
2	25	PHE	PHE	THR	THR	E	E	2 - 249	2 - 249
1	26	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
2	26	PHE	PHE	THR	THR	F	F	2 - 249	2 - 249
1	27	PHE	PHE	ALA	ALA	D	D	2 - 248	2 - 248
2	27	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
1	28	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
2	28	PHE	PHE	THR	THR	H	H	2 - 249	2 - 249
1	29	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
2	29	PHE	PHE	THR	THR	I	I	2 - 249	2 - 249
1	30	PHE	PHE	THR	THR	D	D	2 - 249	2 - 249
2	30	PHE	PHE	THR	THR	J	J	2 - 249	2 - 249
1	31	MET	MET	PRO	PRO	E	E	1 - 250	1 - 250
2	31	MET	MET	PRO	PRO	F	F	1 - 250	1 - 250
1	32	PHE	PHE	ALA	ALA	E	E	2 - 248	2 - 248
2	32	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
1	33	MET	MET	PRO	PRO	E	E	1 - 250	1 - 250
2	33	MET	MET	PRO	PRO	H	H	1 - 250	1 - 250
1	34	MET	MET	PRO	PRO	E	E	1 - 250	1 - 250
2	34	MET	MET	PRO	PRO	I	I	1 - 250	1 - 250
1	35	MET	MET	PRO	PRO	E	E	1 - 250	1 - 250
2	35	MET	MET	PRO	PRO	J	J	1 - 250	1 - 250
1	36	PHE	PHE	ALA	ALA	F	F	2 - 248	2 - 248
2	36	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
1	37	MET	MET	PRO	PRO	F	F	1 - 250	1 - 250
2	37	MET	MET	PRO	PRO	H	H	1 - 250	1 - 250
1	38	MET	MET	PRO	PRO	F	F	1 - 250	1 - 250
2	38	MET	MET	PRO	PRO	I	I	1 - 250	1 - 250
1	39	MET	MET	PRO	PRO	F	F	1 - 250	1 - 250
2	39	MET	MET	PRO	PRO	J	J	1 - 250	1 - 250
1	40	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
2	40	PHE	PHE	ALA	ALA	H	H	2 - 248	2 - 248
1	41	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
2	41	PHE	PHE	ALA	ALA	I	I	2 - 248	2 - 248
1	42	PHE	PHE	ALA	ALA	G	G	2 - 248	2 - 248
2	42	PHE	PHE	ALA	ALA	J	J	2 - 248	2 - 248
1	43	MET	MET	PRO	PRO	H	H	1 - 250	1 - 250
2	43	MET	MET	PRO	PRO	I	I	1 - 250	1 - 250
1	44	MET	MET	PRO	PRO	H	H	1 - 250	1 - 250
2	44	MET	MET	PRO	PRO	J	J	1 - 250	1 - 250
1	45	MET	MET	PRO	PRO	I	I	1 - 250	1 - 250
2	45	MET	MET	PRO	PRO	J	J	1 - 250	1 - 250

NCS ensembles :

Details

asymmetric unit contains two pentamers, chains A-E and F-J

#1: Protein

Nitrite transporter NirC

Mass: 28079.779 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: ST4/74 / Gene: nirC, STM474_3643 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C43 / References: UniProt: E8XEH9

#2: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside /

Octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.22 Å³/Da / Density % sol: 61.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 27% PEG 1000, 0.1 M Nacitrate buffer, 0.4 L of 350 mM, C-HEGA-10, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2011 / Details: mirrors
Radiation	Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→87.75 Å / Num. all: 139064 / Num. obs: 135449 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / R_merge(I) obs: 0.07 / Net I/σ(I): 12

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.6.0117	refinement
XDS		data reduction
XPREP		data reduction

Refinement

Method to determine structure:

MAD
Starting model: PDB entry 3Q7K

3q7k

Resolution: 2.4→87.75 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.921 / SU B: 15.305 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23631	6772	5 %	RANDOM
R_work	0.19232	-	-	-
all	0.19451	132442	-	-
obs	0.19451	128667	97.15 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 49.101 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.36 Å²	0 Å²	0.04 Å²
2-	-	-0.01 Å²	-0 Å²
3-	-	-	-0.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→87.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18780	0	40	196	19016

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.02	19368
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.845	1.93	26506
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.005	5	2486
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.46	22.459	610
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.437	15	2804
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.322	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	3146
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	14156
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	485	-
R_work	0.297	9245	-
obs	-	-	96.74 %

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	1.5372	-0.0164	-0.3765	1.0922	-0.1612	1.5608	0.0714	0.012	0.1346	0.0336	-0.0574	0.0085	-0.3109	0.1393	-0.014	0.0765	-0.0459	-0.0063	0.0381	0.0096	0.0605	35.5092	4.9623	75.4174
2	1.4808	0.012	-0.2539	2.2284	-0.4972	1.304	-0.0732	-0.1084	-0.1224	0.0495	-0.1034	-0.2459	0.167	0.4627	0.1766	0.048	0.051	-0.0111	0.2119	0.0868	0.0856	49.678	-19.7569	82.2742
3	1.5478	-0.0255	-0.1275	1.2646	-0.4008	1.5446	-0.1501	0.0625	-0.3094	-0.2055	-0.0256	-0.0062	0.5914	0.0398	0.1757	0.3545	0.0009	0.0963	0.0346	0.0172	0.1874	30.5868	-41.733	81.0173
4	1.4944	-0.2327	0.106	1.5543	-0.502	1.9538	-0.0547	0.1959	-0.2246	-0.1626	0.1214	0.2885	0.3828	-0.4923	-0.0667	0.1352	-0.1824	-0.016	0.2772	-0.0188	0.2464	4.6632	-30.8176	73.555
5	0.8741	0.2119	0.2233	1.4451	-0.5878	1.5667	0.0349	0.1611	0.0535	0.0526	0.0671	0.2133	-0.1831	-0.4521	-0.102	0.0324	0.0627	-0.0052	0.2511	0.0515	0.1542	7.7201	-1.9377	70.0649
6	1.4673	0.1264	0.0611	1.2369	-0.4711	1.4985	0.019	-0.086	0.2271	0.1914	-0.0414	0.0756	-0.5746	0.0307	0.0224	0.253	-0.0353	-0.0332	0.0342	0.01	0.1388	42.9977	42.1867	20.6936
7	1.3758	0.3214	-0.0485	1.2833	-0.2314	1.1251	-0.0206	-0.0118	0.22	0.026	0.0634	0.3216	-0.3223	-0.4691	-0.0428	0.1021	0.1389	-0.0302	0.246	0.0292	0.2292	16.0935	31.6535	17.7141
8	1.1103	-0.1681	-0.3302	1.6326	-0.531	1.5297	-0.046	-0.0132	-0.06	-0.0606	0.0547	0.1831	0.2123	-0.4493	-0.0087	0.0409	-0.0824	-0.03	0.2026	0.0244	0.1304	17.222	2.7096	22.1197
9	1.1953	0.0159	0.3329	1.2045	-0.1595	1.7957	0.0173	-0.0688	-0.1188	0.01	-0.0528	-0.0126	0.2349	0.0877	0.0355	0.0403	0.0186	0.0091	0.0231	0.0236	0.049	44.928	-4.501	27.7558
10	1.2645	0.0832	0.2325	2.1617	-0.2	1.8315	-0.0043	-0.076	0.0246	0.0564	-0.1137	-0.2374	-0.2428	0.4538	0.118	0.036	-0.0774	-0.0255	0.1933	0.07	0.0752	60.8853	19.9824	26.7014

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 249
2	X-RAY DIFFRACTION	2	B	1 - 250
3	X-RAY DIFFRACTION	3	C	1 - 250
4	X-RAY DIFFRACTION	4	D	2 - 250
5	X-RAY DIFFRACTION	5	E	1 - 250
6	X-RAY DIFFRACTION	6	F	1 - 250
7	X-RAY DIFFRACTION	7	G	2 - 249
8	X-RAY DIFFRACTION	8	H	1 - 250
9	X-RAY DIFFRACTION	9	I	1 - 250
10	X-RAY DIFFRACTION	10	J	1 - 250

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