PDB-3q7k: Formate Channel FocA from Salmonella typhimurium

ID or keywords:

Entry

Database: PDB / ID: 3q7k

Title

Formate Channel FocA from Salmonella typhimurium

Components

Probable formate transporter

Keywords

TRANSPORT PROTEIN /

membrane protein / transport /

cytoplasmic membrane

Function / homology

Function and homology information

formate transport / formate transmembrane transporter activity / plasma membrane => GO:0005886 / membrane => GO:0016020
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

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

Citation

Journal: Science / Year: 2011
Title: pH-dependent gating in a FocA formate channel
Authors: Lu, W. / Du, J. / Wacker, T. / Gerbig-Smentek, E. / Andrade, S.L. / Einsle, O.

History

Deposition	Jan 5, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3q7k.cif.gz	465 KB	Display	PDBx/mmCIF format
PDB format	pdb3q7k.ent.gz	385.7 KB	Display	PDB format
PDBx/mmJSON format	3q7k.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q7/3q7k ftp://data.pdbj.org/pub/pdb/validation_reports/q7/3q7k	HTTPS FTP

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Related structure data

Related structure data	3kcuS S: Starting model for refinement
Similar structure data	3te0-d 3kcu-d 3tds-d 3tdo-d 3i2j-1 4ezc-d 3tdx-d 3te1-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
Related items in Molecule of the Month	#173 - May 2014 Aquaporin similarity (1)

Deposited unit

A: Probable formate transporter

B: Probable formate transporter

C: Probable formate transporter

D: Probable formate transporter

E: Probable formate transporter

G: Probable formate transporter

H: Probable formate transporter

I: Probable formate transporter

J: Probable formate transporter

K: Probable formate transporter

hetero molecules

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

1

A: Probable formate transporter

B: Probable formate transporter

C: Probable formate transporter

D: Probable formate transporter

E: Probable formate transporter

hetero molecules

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

2

G: Probable formate transporter

H: Probable formate transporter

I: Probable formate transporter

J: Probable formate transporter

K: Probable formate transporter

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.951, 205.723, 106.046
Angle α, β, γ (deg.)	90.00, 115.49, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	THR	THR	2	B	B	37 - 91	37 - 91
2	1	1	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	1	TRP	TRP	GLY	GLY	2	B	B	114 - 266	114 - 266
2	2	1	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	2	LEU	LEU	THR	THR	2	C	C	37 - 91	37 - 91
2	1	2	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	2	TRP	TRP	GLY	GLY	2	C	C	114 - 266	114 - 266
2	2	2	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	3	LEU	LEU	THR	THR	2	D	D	37 - 91	37 - 91
2	1	3	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	3	TRP	TRP	GLY	GLY	2	D	D	114 - 266	114 - 266
2	2	3	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	4	LEU	LEU	THR	THR	2	E	E	37 - 91	37 - 91
2	1	4	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	4	TRP	TRP	GLY	GLY	2	E	E	114 - 266	114 - 266
2	2	4	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	5	LEU	LEU	THR	THR	2	G	F	37 - 91	37 - 91
2	1	5	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	5	TRP	TRP	GLY	GLY	2	G	F	114 - 266	114 - 266
2	2	5	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	6	LEU	LEU	THR	THR	2	H	G	37 - 91	37 - 91
2	1	6	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	6	TRP	TRP	GLY	GLY	2	H	G	114 - 266	114 - 266
2	2	6	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	7	LEU	LEU	THR	THR	2	I	H	37 - 91	37 - 91
2	1	7	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	7	TRP	TRP	GLY	GLY	2	I	H	114 - 266	114 - 266
2	2	7	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	8	LEU	LEU	THR	THR	2	J	I	37 - 91	37 - 91
2	1	8	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	8	TRP	TRP	GLY	GLY	2	J	I	114 - 266	114 - 266
2	2	8	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	9	LEU	LEU	THR	THR	2	K	J	37 - 91	37 - 91
2	1	9	LEU	LEU	THR	THR	2	A	A	37 - 91	37 - 91
1	2	9	TRP	TRP	GLY	GLY	2	K	J	114 - 266	114 - 266
2	2	9	TRP	TRP	GLY	GLY	2	A	A	114 - 266	114 - 266
1	1	10	ALA	ALA	LYS	LYS	4	A	A	13 - 33	13 - 33
2	1	10	ALA	ALA	LYS	LYS	4	J	I	13 - 33	13 - 33
1	1	11	ALA	ALA	LYS	LYS	4	C	C	13 - 33	13 - 33
2	1	11	ALA	ALA	LYS	LYS	4	J	I	13 - 33	13 - 33
1	1	12	ALA	ALA	LYS	LYS	4	H	G	13 - 33	13 - 33
2	1	12	ALA	ALA	LYS	LYS	4	J	I	13 - 33	13 - 33
1	1	13	ALA	ALA	LYS	LYS	4	B	B	14 - 33	14 - 33
2	1	13	ALA	ALA	LYS	LYS	4	K	J	14 - 33	14 - 33
1	1	14	ALA	ALA	LYS	LYS	4	D	D	14 - 33	14 - 33
2	1	14	ALA	ALA	LYS	LYS	4	K	J	14 - 33	14 - 33
1	1	15	ALA	ALA	LYS	LYS	4	I	H	14 - 33	14 - 33
2	1	15	ALA	ALA	LYS	LYS	4	K	J	14 - 33	14 - 33
1	1	16	PRO	PRO	THR	THR	4	G	F	31 - 34	31 - 34
2	1	16	PRO	PRO	THR	THR	4	E	E	31 - 34	31 - 34

NCS ensembles :

#1: Protein	Probable formate transporter / Probable formate transporter (Formate channel) Mass: 32061.805 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria) Strain: CT18 / Gene: focA, STY0974, t1960 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)C43 / References: UniProt: Q8XF76, UniProt: Q7CQU0*PLUS
#2: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.25 Å³/Da / Density % sol: 62.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: PEG 400, lithium sulfate, sodium citrate, pH 4.0, 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: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2010 / 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: 2.8→48.8 Å / Num. all: 100520 / Num. obs: 92780 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / B_iso Wilson estimate: 48.3 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 7.8

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.5.0110	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KCU

3kcu

Resolution: 2.8→43.64 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.881 / SU B: 12.212 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25366	4664	5 %	RANDOM
R_work	0.21856	-	-	-
obs	0.22034	88073	92.22 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 48.328 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.33 Å²	0 Å²	-2.61 Å²
2-	-	-1.63 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→43.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19100	0	39	12	19151

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	19609
X-RAY DIFFRACTION	r_angle_refined_deg	1.837	1.948	26641
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.649	5	2507
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.094	23.382	621
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.163	15	3140
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.575	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	3181
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	14097
X-RAY DIFFRACTION	r_mcbond_it	0.648	1.5	12459
X-RAY DIFFRACTION	r_mcangle_it	1.246	2	19975
X-RAY DIFFRACTION	r_scbond_it	1.771	3	7150
X-RAY DIFFRACTION	r_scangle_it	2.935	4.5	6666

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	B	832	TIGHT POSITIONAL	0.06	0.05
1	B	743	MEDIUM POSITIONAL	0.07	0.5
1	B	832	TIGHT THERMAL	0.16	0.5
1	B	743	MEDIUM THERMAL	0.2	2
2	C	832	TIGHT POSITIONAL	0.07	0.05
2	C	743	MEDIUM POSITIONAL	0.08	0.5
2	C	832	TIGHT THERMAL	0.16	0.5
2	C	743	MEDIUM THERMAL	0.2	2
3	D	832	TIGHT POSITIONAL	0.06	0.05
3	D	743	MEDIUM POSITIONAL	0.08	0.5
3	D	832	TIGHT THERMAL	0.16	0.5
3	D	743	MEDIUM THERMAL	0.21	2
4	E	832	TIGHT POSITIONAL	0.06	0.05
4	E	743	MEDIUM POSITIONAL	0.08	0.5
4	E	832	TIGHT THERMAL	0.2	0.5
4	E	743	MEDIUM THERMAL	0.23	2
5	G	832	TIGHT POSITIONAL	0.06	0.05
5	G	743	MEDIUM POSITIONAL	0.07	0.5
5	G	832	TIGHT THERMAL	0.2	0.5
5	G	743	MEDIUM THERMAL	0.23	2
6	H	832	TIGHT POSITIONAL	0.05	0.05
6	H	743	MEDIUM POSITIONAL	0.08	0.5
6	H	832	TIGHT THERMAL	0.18	0.5
6	H	743	MEDIUM THERMAL	0.24	2
7	I	832	TIGHT POSITIONAL	0.06	0.05
7	I	743	MEDIUM POSITIONAL	0.07	0.5
7	I	832	TIGHT THERMAL	0.16	0.5
7	I	743	MEDIUM THERMAL	0.2	2
8	J	832	TIGHT POSITIONAL	0.06	0.05
8	J	743	MEDIUM POSITIONAL	0.08	0.5
8	J	832	TIGHT THERMAL	0.17	0.5
8	J	743	MEDIUM THERMAL	0.19	2
9	K	832	TIGHT POSITIONAL	0.06	0.05
9	K	743	MEDIUM POSITIONAL	0.08	0.5
9	K	832	TIGHT THERMAL	0.15	0.5
9	K	743	MEDIUM THERMAL	0.2	2
10	A	154	MEDIUM POSITIONAL	0.86	0.5
10	A	154	MEDIUM THERMAL	0.55	2
11	C	154	MEDIUM POSITIONAL	0.55	0.5
11	C	154	MEDIUM THERMAL	0.53	2
12	H	154	MEDIUM POSITIONAL	0.85	0.5
12	H	154	MEDIUM THERMAL	0.46	2
13	B	149	MEDIUM POSITIONAL	1.9	0.5
13	B	149	MEDIUM THERMAL	0.41	2
14	D	136	MEDIUM POSITIONAL	0.96	0.5
14	D	136	MEDIUM THERMAL	0.48	2
15	I	149	MEDIUM POSITIONAL	1.93	0.5
15	I	149	MEDIUM THERMAL	0.56	2
16	G	31	MEDIUM POSITIONAL	0.78	0.5
16	G	31	MEDIUM THERMAL	0.58	2

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	363	-
R_work	0.281	6652	-
obs	-	-	94.27 %

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