PDB-2vv5: The open structure of MscS

ID or keywords:

Entry

Database: PDB / ID: 2vv5

Title

The open structure of MscS

Components

SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

Keywords

MEMBRANE PROTEIN / ION TRANSPORT / TRANSMEMBRANE / INNER MEMBRANE / MEMBRANE STRUCTURE / MEMBRANE / TRANSPORT / OPEN CHANNEL / IONIC CHANNEL

Function / homology

Function and homology information

intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / protein homooligomerization / monoatomic ion transmembrane transport / identical protein binding / membrane / plasma membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.45 Å

Authors

Wang, W. / Dong, C. / Johnson, K.A. / Naismith, J.H.

Citation

Journal: Science / Year: 2008
Title: The Structure of an Open Form of an E. Coli Mechanosensitive Channel at 3.45 A Resolution.
Authors: Wang, W. / Black, S.S. / Edwards, M.D. / Miller, S. / Morrison, E.L. / Bartlett, W. / Dong, C. / Naismith, J.H. / Booth, I.R.

History

Deposition	Jun 3, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vv5.cif.gz	328.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2vv5.ent.gz	270.8 KB	Display	PDB format
PDBx/mmJSON format	2vv5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/2vv5 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vv5	HTTPS FTP

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Related structure data

Related structure data	2oauS S: Starting model for refinement
Similar structure data	2oau-d 5aji-d 4zru-d 4agf-d 4hw9-d 4age-d 5bp0-d 5j5g-d 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	#107 - Nov 2008 Mechanosensitive Channels similarity (13) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

B: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

C: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

D: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

E: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

F: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

G: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL

217 kDa, 7 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)	230.880, 126.620, 123.220
Angle α, β, γ (deg.)	90.00, 90.42, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
6	2	F
7	2	G

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	ALA	ALA	ASP	ASP	1	A	A	66 - 218	66 - 218
2	1	1	ALA	ALA	ASP	ASP	1	B	B	66 - 218	66 - 218
3	1	1	ALA	ALA	ASP	ASP	1	C	C	66 - 218	66 - 218
4	1	1	ALA	ALA	ASP	ASP	1	D	D	66 - 218	66 - 218
5	1	1	ALA	ALA	ASP	ASP	1	E	E	66 - 218	66 - 218
6	1	1	ALA	ALA	ASP	ASP	1	F	F	66 - 218	66 - 218
7	1	1	ALA	ALA	ASP	ASP	1	G	G	66 - 218	66 - 218
1	2	1	ARG	ARG	ARG	ARG	2	A	A	219	219
2	2	1	ARG	ARG	ARG	ARG	2	B	B	219	219
3	2	1	ARG	ARG	ARG	ARG	2	C	C	219	219
4	2	1	ARG	ARG	ARG	ARG	2	D	D	219	219
5	2	1	ARG	ARG	ARG	ARG	2	E	E	219	219
6	2	1	ARG	ARG	ARG	ARG	2	F	F	219	219
7	2	1	ARG	ARG	ARG	ARG	2	G	G	219	219
1	3	1	GLU	GLU	VAL	VAL	1	A	A	220 - 280	220 - 280
2	3	1	GLU	GLU	VAL	VAL	1	B	B	220 - 280	220 - 280
3	3	1	GLU	GLU	VAL	VAL	1	C	C	220 - 280	220 - 280
4	3	1	GLU	GLU	VAL	VAL	1	D	D	220 - 280	220 - 280
5	3	1	GLU	GLU	VAL	VAL	1	E	E	220 - 280	220 - 280
6	3	1	GLU	GLU	VAL	VAL	1	F	F	220 - 280	220 - 280
7	3	1	GLU	GLU	VAL	VAL	1	G	G	220 - 280	220 - 280
1	1	2	LEU	LEU	VAL	VAL	2	A	A	25 - 65	25 - 65
2	1	2	LEU	LEU	VAL	VAL	2	B	B	25 - 65	25 - 65
3	1	2	LEU	LEU	VAL	VAL	2	C	C	25 - 65	25 - 65
4	1	2	LEU	LEU	VAL	VAL	2	D	D	25 - 65	25 - 65
5	1	2	LEU	LEU	VAL	VAL	2	E	E	25 - 65	25 - 65
6	1	2	LEU	LEU	VAL	VAL	2	F	F	25 - 65	25 - 65
7	1	2	LEU	LEU	VAL	VAL	2	G	G	25 - 65	25 - 65

NCS ensembles :

ID
1
2

#1: Protein	SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL / MSCS Mass: 30950.953 Da / Num. of mol.: 7 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C0S2, UniProt: P0C0S1*PLUS
Compound details	ENGINEERED RESIDUE IN CHAIN A, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 106 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN C, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN D, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN E, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN F, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN G, ALA 106 TO VAL

#1: Protein

SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL / MSCS

Mass: 30950.953 Da / Num. of mol.: 7 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Production host:

ESCHERICHIA COLI (E. coli) / References: UniProt: P0C0S2, UniProt: P0C0S1*PLUS

Compound details

ENGINEERED RESIDUE IN CHAIN A, ALA 106 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 106 TO VAL ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.7 Å³/Da / Density % sol: 73.61 % / Description: NONE
Crystal grow	pH: 7.5 Details: THE BEST CRYSTALS (BY VISUAL INSPECTION) WERE OBTAINED USING 0.1M HEPES PH 7.2, 0.2 M SODIUM FORMATE, 14 % PEG3350, 8 % GLYCEROL AS PRECIPITANT. PRIOR TO DATA COLLECTION, CRYSTALS WERE ...Details: THE BEST CRYSTALS (BY VISUAL INSPECTION) WERE OBTAINED USING 0.1M HEPES PH 7.2, 0.2 M SODIUM FORMATE, 14 % PEG3350, 8 % GLYCEROL AS PRECIPITANT. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO A SOLUTION CONTAINING 40MM TRIS PH 7.5, 0.01% FOS-CHOLINE-14, 0.15 M NACL, 0.3 M SODIUM FORMATE, 20% GLYCEROL AND 22% PEG3350.

Crystal

Density Matthews: 4.7 Å³/Da / Density % sol: 73.61 % / Description: NONE

Crystal grow

pH: 7.5
Details: THE BEST CRYSTALS (BY VISUAL INSPECTION) WERE OBTAINED USING 0.1M HEPES PH 7.2, 0.2 M SODIUM FORMATE, 14 % PEG3350, 8 % GLYCEROL AS PRECIPITANT. PRIOR TO DATA COLLECTION, CRYSTALS WERE ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 3.45→37 Å / Num. obs: 46433 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shell	Resolution: 3.45→3.55 Å / Redundancy: 4 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OAU

2oau

Resolution: 3.45→123.09 Å / Cor.coef. F_o:F_c: 0.882 / Cor.coef. F_o:F_c free: 0.887 / SU B: 77.976 / SU ML: 0.534 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.612 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.312	2336	5 %	RANDOM
R_work	0.293	-	-	-
obs	0.294	44094	99 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 92.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.67 Å²	0 Å²	10.14 Å²
2-	-	-3.68 Å²	0 Å²
3-	-	-	4.49 Å²

Refinement step

Cycle: LAST / Resolution: 3.45→123.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13692	0	0	0	13692

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	13867
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9233
X-RAY DIFFRACTION	r_angle_refined_deg	1.247	1.963	18809
X-RAY DIFFRACTION	r_angle_other_deg	0.925	3	22477
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.367	5	1785
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.27	23.125	560
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.076	15	2408
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.399	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	2310
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	15407
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2877
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	3076
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	9535
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	7135
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	7992
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	253
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	0.368	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.469	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.433	0.2	3
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	0.435	1.5	11490
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.476	2	14315
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.721	3	5723
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.078	4.5	4494
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2756	tight positional	0.03	0.05
1	2	B	2756	tight positional	0.03	0.05
1	3	C	2756	tight positional	0.03	0.05
1	4	D	2756	tight positional	0.02	0.05
1	5	E	2756	tight positional	0.02	0.05
1	6	F	2756	tight positional	0.02	0.05
1	7	G	2756	tight positional	0.02	0.05
2	1	A	244	tight positional	0.02	0.05
2	2	B	244	tight positional	0.02	0.05
2	3	C	244	tight positional	0.02	0.05
2	4	D	244	tight positional	0.02	0.05
2	5	E	244	tight positional	0.02	0.05
2	6	F	244	tight positional	0.02	0.05
2	7	G	244	tight positional	0.02	0.05
1	1	A	18	medium positional	0.92	0.5
1	2	B	18	medium positional	1.9	0.5
1	3	C	18	medium positional	1.27	0.5
1	4	D	18	medium positional	0.92	0.5
1	5	E	18	medium positional	0.91	0.5
1	6	F	18	medium positional	1.45	0.5
1	7	G	18	medium positional	1.46	0.5
2	1	A	257	medium positional	0.62	0.5
2	2	B	257	medium positional	0.43	0.5
2	3	C	257	medium positional	0.42	0.5
2	4	D	257	medium positional	0.48	0.5
2	5	E	257	medium positional	0.42	0.5
2	6	F	257	medium positional	0.67	0.5
2	7	G	257	medium positional	0.49	0.5
1	1	A	2756	tight thermal	0.04	0.5
1	2	B	2756	tight thermal	0.04	0.5
1	3	C	2756	tight thermal	0.04	0.5
1	4	D	2756	tight thermal	0.04	0.5
1	5	E	2756	tight thermal	0.04	0.5
1	6	F	2756	tight thermal	0.03	0.5
1	7	G	2756	tight thermal	0.04	0.5
2	1	A	244	tight thermal	0.03	0.5
2	2	B	244	tight thermal	0.03	0.5
2	3	C	244	tight thermal	0.03	0.5
2	4	D	244	tight thermal	0.02	0.5
2	5	E	244	tight thermal	0.02	0.5
2	6	F	244	tight thermal	0.02	0.5
2	7	G	244	tight thermal	0.02	0.5
1	1	A	18	medium thermal	0.27	2
1	2	B	18	medium thermal	0.56	2
1	3	C	18	medium thermal	0.2	2
1	4	D	18	medium thermal	0.21	2
1	5	E	18	medium thermal	0.26	2
1	6	F	18	medium thermal	0.29	2
1	7	G	18	medium thermal	0.17	2
2	1	A	257	medium thermal	0.16	2
2	2	B	257	medium thermal	0.17	2
2	3	C	257	medium thermal	0.16	2
2	4	D	257	medium thermal	0.12	2
2	5	E	257	medium thermal	0.13	2
2	6	F	257	medium thermal	0.13	2
2	7	G	257	medium thermal	0.12	2

LS refinement shell

Resolution: 3.45→3.54 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.369	200
R_work	0.381	3242

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	3.592	-0.0059	-0.8804	2.9461	0.1772	3.1402	-0.1571	0.7785	0.0826	-0.7291	0.2806	-0.4568	0.1468	0.3571	-0.1235	-0.4543	0.0616	0.1268	-0.2285	-0.0369	-0.2994	82.622	-28.455	18.74
2	1.3679	-0.2208	-0.4401	1.2334	-0.1246	1.5177	-0.0572	0.718	0.0134	-0.5575	0.0442	-0.3408	0.0846	0.1885	0.0129	-0.4184	0.0447	0.0162	-0.1588	0.0106	-0.3038	74.499	-28.456	24.37
3	1.9492	0.1093	-0.0261	2.8605	0.4226	1.829	0.0054	0.4693	0.102	-0.2311	-0.0542	0.2752	0.1579	-0.2209	0.0488	-0.5611	0.0506	-0.2246	-0.5733	0.0473	-0.5121	53.788	-28.422	38.86
4	1.8482	-0.0344	-0.0666	2.369	0.1289	1.4501	0.0169	0.0788	0.0119	0.0848	-0.0478	0.7086	0.1001	-0.5643	0.0309	-0.7212	0.0145	-0.0696	-0.5187	0.002	-0.1464	29.209	-28.378	56.037

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 89
2	X-RAY DIFFRACTION	1	B	25 - 89
3	X-RAY DIFFRACTION	1	C	25 - 89
4	X-RAY DIFFRACTION	1	D	25 - 89
5	X-RAY DIFFRACTION	1	E	25 - 89
6	X-RAY DIFFRACTION	1	F	25 - 89
7	X-RAY DIFFRACTION	1	G	25 - 89
8	X-RAY DIFFRACTION	2	A	90 - 126
9	X-RAY DIFFRACTION	2	B	90 - 126
10	X-RAY DIFFRACTION	2	C	90 - 126
11	X-RAY DIFFRACTION	2	D	90 - 126
12	X-RAY DIFFRACTION	2	E	90 - 126
13	X-RAY DIFFRACTION	2	F	90 - 126
14	X-RAY DIFFRACTION	2	G	90 - 126
15	X-RAY DIFFRACTION	3	A	127 - 180
16	X-RAY DIFFRACTION	3	B	127 - 180
17	X-RAY DIFFRACTION	3	C	127 - 180
18	X-RAY DIFFRACTION	3	D	127 - 180
19	X-RAY DIFFRACTION	3	E	127 - 180
20	X-RAY DIFFRACTION	3	F	127 - 180
21	X-RAY DIFFRACTION	3	G	127 - 180
22	X-RAY DIFFRACTION	4	A	181 - 280
23	X-RAY DIFFRACTION	4	B	181 - 280
24	X-RAY DIFFRACTION	4	C	181 - 280
25	X-RAY DIFFRACTION	4	D	181 - 280
26	X-RAY DIFFRACTION	4	E	181 - 280
27	X-RAY DIFFRACTION	4	F	181 - 280
28	X-RAY DIFFRACTION	4	G	181 - 280

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