PDB-2xg6: Molecular insights into clinically isolated OmpC mutants and thei...

ID or keywords:

Entry

Database: PDB / ID: 2xg6

Title

Molecular insights into clinically isolated OmpC mutants and their role in multi-drug resistance

Components

OMPC

Keywords

TRANSPORT PROTEIN / PORIN

Function / homology

Function and homology information

porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.47 Å

Authors

Lou, H. / Naismith, J.H.

Citation

Journal: Plos One / Year: 2011
Title: Altered Antibiotic Transport in Ompc Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. Coli.
Authors: Lou, H. / Chen, M. / Black, S.S. / Bushell, S.R. / Ceccarelli, M. / Mach, T. / Beis, K. / Low, A.S. / Bamford, V.A. / Booth, I.R. / Bayley, H. / Naismith, J.H.

History

Deposition	May 31, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 14, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 16, 2011	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site 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_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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Download

PDBx/mmCIF format	2xg6.cif.gz	397.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2xg6.ent.gz	331 KB	Display	PDB format
PDBx/mmJSON format	2xg6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2xg6_validation.pdf.gz	500.7 KB	Display	wwPDB validaton report
Full document	2xg6_full_validation.pdf.gz	561.5 KB	Display
Data in XML	2xg6_validation.xml.gz	70.4 KB	Display
Data in CIF	2xg6_validation.cif.gz	93.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/2xg6 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xg6	HTTPS FTP

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Related structure data

Related structure data	2xe1SC 2xe2C 2xe3C 2xe5C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2xe3-2 2j1n-d 6rck-d 3hw9-1 3k19-1 1pho-1 2xe5-1 1hxx-1 2xe3-1 6rcp-1 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: OMPC

B: OMPC

C: OMPC

D: OMPC

E: OMPC

F: OMPC

hetero molecules

230 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: OMPC

E: OMPC

F: OMPC

hetero molecules

defined by author&software
115 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: OMPC

B: OMPC

C: OMPC

hetero molecules

defined by author&software
115 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.820, 159.725, 164.601
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	OMPC Mass: 38337.273 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Description: DERIVED FROM O6 UROPATHOGENIC STRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9K597
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
Sequence details	NOTE THIS CLINICAL ISOLATE HAS MUTANTS D18E, S271F, R124H

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 69.87 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
Detector	Type: ADSC QUANTUM 210 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.93 Å / Relative weight: 1
Reflection	Resolution: 3.47→54 Å / Num. obs: 40939 / % possible obs: 84.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / B_iso Wilson estimate: 94 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 7.1
Reflection shell	Resolution: 3.47→3.7 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 73

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0073	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XE1

2xe1

Resolution: 3.47→53.19 Å / Cor.coef. F_o:F_c: 0.891 / Cor.coef. F_o:F_c free: 0.862 / SU B: 87.244 / SU ML: 0.566 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.717 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THIS USED NEW REFMAC5 (V5.6) OPTION NSCR LOCAL.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29306	2053	5 %	RANDOM
R_work	0.2612	-	-	-
obs	0.26278	38636	82.41 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 47.027 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.15 Å²	-0 Å²	-0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 3.47→53.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16284	0	15	0	16299

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.021	16674
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	10824
X-RAY DIFFRACTION	r_angle_refined_deg	0.948	1.921	22578
X-RAY DIFFRACTION	r_angle_other_deg	0.817	3	26100
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.09	5	2052
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.232	25.031	966
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.005	15	2508
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.33	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2250
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	19590
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3780
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_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

LS refinement shell

Resolution: 3.47→3.56 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	138	-
R_work	0.327	2045	-
obs	-	-	60.64 %

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	4.2519	0.7591	0.9117	3.5149	-1.0635	2.8967	-0.2089	-0.6707	-0.1101	0.6616	-0.294	-0.694	-1.0614	1.0903	0.5029	1.5846	-0.2612	-0.2556	1.069	0.0467	0.3243	53.432	30.575	63.608
2	4.2976	1.0829	2.6056	5.6353	-1.734	3.1479	0.113	-0.6485	-0.1471	1.1802	-0.6605	-0.828	-1.2433	0.3938	0.5475	2.0438	-0.4934	-0.5487	1.5167	0.1201	0.6825	63.075	33.327	74.611
3	4.3687	0.9835	0.8237	2.1334	0.326	2.1374	0.0712	-0.8342	-0.8874	0.766	-0.1514	-0.9645	0.1308	1.0821	0.0803	1.5878	0.1194	-0.2797	1.3304	0.4067	0.6231	59.877	15.657	72.653
4	4.2067	0.3742	-0.9815	3.4078	-0.0004	1.5165	-0.3528	-0.3818	-0.1944	0.6896	0.2418	0.6398	-0.0279	-0.8599	0.1111	1.5861	0.0863	0.1847	0.8863	0.0927	0.175	25.769	22.152	63.287
5	45.5377	17.9678	50.5352	7.127	19.004	92.4394	2.9494	-0.1449	-1.7364	1.2271	0.1805	-0.6762	4.7209	-2.0679	-3.1299	3.2519	0.0792	-0.1788	2.1729	0.9245	1.2499	34.644	11.516	81.495
6	2.2548	0.5478	-0.6108	3.9174	-0.7909	3.4697	-0.0268	-0.8921	-0.3978	0.7872	0.1783	0.9754	-0.0848	-1.2511	-0.1515	1.5059	0.1488	0.464	1.6042	0.1899	0.5307	12.871	20.4	73.402
7	3.9951	-0.2941	-0.1596	2.5451	-0.1836	1.3193	-0.1744	-0.9168	0.9687	0.8682	0.0222	0.313	-1.4929	-0.1724	0.1522	2.3492	0.2676	-0.0697	0.7679	-0.4294	0.4936	29.941	51.421	68.606
8	5.0977	-1.8688	0.7975	4.8786	-2.5683	1.6208	-0.24	-0.8716	1.3575	1.289	0.2169	-0.092	-1.587	0.0401	0.0232	3.4641	-0.2989	-0.1672	0.7377	-0.8211	1.1942	38.728	65.944	70.305
9	3.0371	-3.3859	-2.9069	4.5623	4.7846	14.1725	-0.5052	-1.0295	1.2387	1.3973	0.5238	-0.8464	-0.2447	-0.6297	-0.0186	2.9526	-0.5195	-0.1988	1.1685	-0.7865	1.0744	46.722	59.671	76.56
10	5.9617	0.3486	0.9217	4.1723	-0.5205	3.8812	-0.4153	-0.8933	-0.0122	0.3526	0.0403	-0.5514	-0.8049	0.713	0.375	1.6267	-0.0796	-0.1734	0.842	-0.159	0.2235	117.501	108.932	62.589
11	5.9186	-0.3842	-3.8552	8.0222	-1.1943	10.1704	-0.1847	-1.0123	0.7579	0.386	-0.0094	-0.8218	-0.2885	1.51	0.1941	1.6597	-0.4785	-0.5062	1.2661	-0.2806	0.5597	131.733	114.09	66.323
12	3.7215	0.2744	1.1001	2.4289	0.6436	4.0404	0.0295	-0.8588	-0.5026	0.781	0.0662	-1.1145	-0.1331	1.219	-0.0957	1.5155	0.0771	-0.3206	1.2659	0.1102	0.5921	128.214	99	72.851
13	4.2843	0.0228	0.3184	4.2565	0.0339	1.5613	-0.516	-0.8897	-0.2542	0.7214	0.2382	0.5985	0.084	-1.3128	0.2778	1.5178	0.0955	0.241	1.3896	-0.0618	0.2905	93.159	100.841	65.253
14	3.1181	0.6355	2.9083	3.4668	0.0089	10.6977	0.0731	-1.4417	-0.5589	1.0651	-0.1218	0.515	0.7547	-2.054	0.0487	1.476	0.013	0.5147	2.2371	0.0976	0.4959	82.906	94.448	77.413
15	2.8068	1.883	0.2489	5.5604	-2.5273	3.315	-0.0852	-1.2529	0.3126	0.7792	0.0104	1.3738	-0.454	-2.1814	0.0748	1.4556	0.5462	0.5636	2.9754	-0.5283	0.798	76.519	110.127	71.922
16	4.4145	-1.0764	-0.1607	3.0826	0.881	2.7571	-0.2852	-1.0112	1.1326	0.4873	0.0043	0.1424	-1.7074	-0.5879	0.2809	2.2033	0.4538	-0.2244	0.9113	-0.6011	0.5839	99.447	131.915	66.339
17	7.3915	1.3503	-6.3362	2.9656	-6.1925	20.4592	-0.4924	-1.6307	1.7356	0.6713	0.2729	-0.0341	-2.6223	-0.4516	0.2195	3.3232	0.325	-0.2487	1.0645	-1.1794	1.3482	104.359	144.962	73.533
18	2.5563	-1.5992	-0.5026	3.1524	0.1545	1.8133	-0.2928	-0.979	1.2943	0.8755	0.2135	-0.2911	-1.1579	-0.0558	0.0794	3.003	-0.2174	-0.5153	1.2704	-0.8661	1.1588	116.411	140.552	74.098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 154
2	X-RAY DIFFRACTION	2	A	155 - 201
3	X-RAY DIFFRACTION	3	A	202 - 343
4	X-RAY DIFFRACTION	4	B	1 - 148
5	X-RAY DIFFRACTION	5	B	149 - 161
6	X-RAY DIFFRACTION	6	B	162 - 343
7	X-RAY DIFFRACTION	7	C	1 - 215
8	X-RAY DIFFRACTION	8	C	216 - 277
9	X-RAY DIFFRACTION	9	C	278 - 343
10	X-RAY DIFFRACTION	10	D	1 - 114
11	X-RAY DIFFRACTION	11	D	115 - 157
12	X-RAY DIFFRACTION	12	D	158 - 343
13	X-RAY DIFFRACTION	13	E	1 - 196
14	X-RAY DIFFRACTION	14	E	197 - 254
15	X-RAY DIFFRACTION	15	E	255 - 343
16	X-RAY DIFFRACTION	16	F	1 - 201
17	X-RAY DIFFRACTION	17	F	202 - 266
18	X-RAY DIFFRACTION	18	F	267 - 343

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