PDB-5ldt: Crystal Structures of MOMP from Campylobacter jejuni

ID or keywords:

Entry

Database: PDB / ID: 5ldt

Title

Crystal Structures of MOMP from Campylobacter jejuni

Components

MOMP porin

Keywords

MEMBRANE PROTEIN / outermenbrane protein / porin

Function / homology

Campylobacter major outer membrane / Campylobacter major outer membrane protein / metal ion binding / MOMP porin

Function and homology information

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.88 Å

Authors

Ferrara, L.G.M. / Wallat, G.D. / Moynie, L. / Naismith, J.H.

Funding support

United Kingdom, 1items

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded beta-Barrel Monomers with a Ca(2+) Ion Bound at the Constriction Zone.
Authors: Ferrara, L.G. / Wallat, G.D. / Moynie, L. / Dhanasekar, N.N. / Aliouane, S. / Acosta-Gutierrez, S. / Pages, J.M. / Bolla, J.M. / Winterhalter, M. / Ceccarelli, M. / Naismith, J.H.

History

Deposition	Jun 27, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	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_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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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Download

PDBx/mmCIF format	5ldt.cif.gz	469 KB	Display	PDBx/mmCIF format
PDB format	pdb5ldt.ent.gz	390.3 KB	Display	PDB format
PDBx/mmJSON format	5ldt.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/ld/5ldt ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldt	HTTPS FTP

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Related structure data

Related structure data	5ldvSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ldv-1 4c0c-1 2c39-1 2c37-2 3gll-1 2br2-3 2c37-1 5l2b-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

Deposited unit

A: MOMP porin

B: MOMP porin

C: MOMP porin

hetero molecules

133 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	94.360, 99.330, 172.140
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 405 / Label seq-ID: 1 - 405

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	B	B
2	3	C	C

NCS ensembles :

ID
1
2
3

#1: Protein	MOMP porin Mass: 43930.926 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / References: UniProt: Q659I5
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.06 Å³/Da / Density % sol: 59.81 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05M calcium chloride, 0.05M barium chloride, 0.1M Tris pH 7.5, 30% (v/v) PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.88→47.72 Å / Num. obs: 36693 / % possible obs: 99.84 % / Redundancy: 7.3 % / R_merge(I) obs: 0.14 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.88→2.9 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 3 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0124	refinement
xia2		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LDV

5ldv

Resolution: 2.88→47.72 Å / Cor.coef. F_o:F_c: 0.894 / Cor.coef. F_o:F_c free: 0.86 / SU B: 36.271 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27192	1865	5 %	RANDOM
R_work	0.23764	-	-	-
obs	0.23931	35440	99.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.15 Å

Displacement parameters

B_iso mean: 48.122 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.65 Å²	0 Å²	0 Å²
2-	-	-3.31 Å²	0 Å²
3-	-	-	3.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.88→47.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9270	0	44	13	9327

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	9535
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	8655
X-RAY DIFFRACTION	r_angle_refined_deg	1.607	1.934	12887
X-RAY DIFFRACTION	r_angle_other_deg	1.181	3	19801
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.519	5	1209
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.074	25.5	480
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.661	15	1440
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.601	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1404
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	11297
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	2348
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	0.594	1.478	4845
X-RAY DIFFRACTION	r_mcbond_other	0.594	1.478	4844
X-RAY DIFFRACTION	r_mcangle_it	0.896	2.215	6036
X-RAY DIFFRACTION	r_mcangle_other	0.896	2.215	6037
X-RAY DIFFRACTION	r_scbond_it	0.657	1.533	4690
X-RAY DIFFRACTION	r_scbond_other	0.656	1.533	4690
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.862	2.27	6849
X-RAY DIFFRACTION	r_long_range_B_refined	2.612	11.616	9869
X-RAY DIFFRACTION	r_long_range_B_other	2.612	11.618	9870
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	44764	0.04
1	2	B	44764	0.04
2	1	A	45180	0.04
2	2	C	45180	0.04
3	1	B	44694	0.05
3	2	C	44694	0.05

LS refinement shell

Resolution: 2.88→2.955 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	140	-
R_work	0.345	2568	-
obs	-	-	99.78 %

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	1.7824	0.986	0.1118	2.0375	0.1745	1.7437	0.1265	-0.0642	-0.1988	0.3512	-0.0547	-0.3898	0.05	0.1352	-0.0719	0.0676	0.0109	-0.0682	0.3662	-0.0112	0.1075	-11.866	2.767	-32.575
2	1.1816	0.2432	0.2447	2.0804	0.087	1.3192	0.0257	-0.0785	0.0514	-0.1046	-0.0767	-0.1767	-0.0267	-0.0021	0.051	0.0304	0.0122	0.0209	0.3591	-0.0114	0.027	-13.768	7.666	-45.689
3	15.5827	-7.5856	6.4452	4.2694	-1.8215	6.0357	0.7568	-0.069	-0.6584	-0.3771	-0.0528	0.0057	0.5911	-0.0614	-0.7039	0.4252	0.1246	0.1109	0.5292	0.0117	0.5488	3.303	-9.495	-58.199
4	4.3915	-0.0384	0.9549	2.3172	-0.965	2.9064	0.0194	0.3025	-0.1919	-0.4434	0.0539	-0.3401	0.3129	0.2629	-0.0733	0.1616	-0.0283	0.1106	0.4022	-0.1129	0.1231	1.253	7.759	-55.098
5	1.5458	-0.5792	0.797	2.682	-0.5296	2.5237	-0.0199	0.0394	-0.3074	-0.1085	-0.0974	-0.5681	-0.1496	0.2616	0.1173	0.0218	-0.0606	0.0259	0.4527	-0.0113	0.2888	5.991	11.807	-46.053
6	1.2045	0.5954	-0.2928	2.0155	-0.6792	1.0962	0.0296	-0.0592	-0.1993	0.2673	-0.07	-0.664	-0.1656	0.3454	0.0403	0.0779	-0.0613	-0.0722	0.5761	-0.0707	0.3677	7.909	10.806	-35.286
7	1.7643	-0.5205	0.2261	2.2044	-0.3328	0.878	0.1064	0.0515	0.1665	-0.1078	-0.2096	-0.1523	0.0617	0.0747	0.1032	0.0533	0.0123	0.0271	0.3164	-0.0472	0.0436	-34.351	3.287	-37.042
8	1.6023	-1.0781	0.7473	1.8226	-1.0421	2.0578	0.1106	-0.2165	-0.14	0.1149	0.2603	0.6473	0.0915	-0.3307	-0.3709	0.094	0.0069	0.0778	0.4644	0.0277	0.2989	-51.207	3.488	-27.687
9	2.8543	-1.5427	-1.5059	3.841	0.8438	4.6841	-0.115	-0.0234	-0.4497	0.1344	0.2477	1.2487	0.3314	-0.3573	-0.1327	0.0522	-0.002	-0.0463	0.5806	0.129	0.7879	-62.103	4.573	-41.873
10	0.0261	-0.1288	0.3201	7.4734	-0.6317	4.2996	0.013	-0.0203	-0.0388	-0.2378	0.1164	1.4046	0.0535	-0.255	-0.1294	0.0414	0.0115	-0.0243	0.4393	0.0364	0.4719	-55.888	13.418	-40.866
11	2.3167	-1.3101	-0.056	7.5294	1.6023	5.0157	0.2249	0.1862	-0.2221	-1.21	0.0469	1.6189	-0.1954	-0.3101	-0.2718	0.2931	-0.0239	-0.3215	0.4385	0.099	0.5266	-55.411	8.079	-52.629
12	3.6226	-5.7224	0.7456	9.5698	-1.3043	0.7235	0.3259	0.0595	-0.2704	-0.8302	0.0169	0.5662	0.1205	-0.1172	-0.3428	0.218	-0.0317	-0.102	0.3228	0.0117	0.1886	-45.221	7.55	-52.156
13	1.0178	-0.1824	-0.0811	2.1591	0.6532	1.8831	0.0375	-0.0836	-0.0389	0.2039	-0.0908	0.0435	-0.1785	-0.0781	0.0533	0.2099	-0.0382	0.0157	0.402	0.0026	0.0197	-26.635	2.476	-15.031
14	2.9838	-0.1623	-0.8912	0.3229	0.5598	2.0286	-0.1468	-0.3822	-0.1621	0.2388	0.0267	-0.0919	-0.1018	0.3072	0.1202	0.4897	-0.0753	-0.1723	0.6267	0.033	0.1361	-11.244	5.701	-2.956
15	6.7489	1.1168	-0.4884	0.7873	0.9395	2.0954	0.0609	-0.6709	-0.7366	0.3564	0.0514	-0.3446	0.1894	0.1568	-0.1122	0.7831	0.064	-0.3505	0.9128	-0.0224	0.2905	-18.279	4.467	12.131
16	3.1925	0.5129	1.2646	7.3468	1.7636	0.9607	0.0186	-0.4393	0.3082	0.5391	-0.1053	-0.0465	-0.0272	0.0666	0.0867	0.6632	-0.0333	0.0015	0.7189	-0.067	0.032	-22.369	13.52	6.374
17	2.4484	2.4779	2.2822	6.7507	1.517	3.4203	-0.2674	-0.3349	-0.2524	0.5078	0.3902	0.3229	0.0075	0.0835	-0.1228	0.5448	0.1513	0.2356	0.7251	0.1411	0.1916	-34.593	0.104	11.298
18	1.8823	0.7738	0.4062	5.4255	3.2623	3.2441	-0.0723	-0.4516	0.1344	0.5244	0.0295	-0.0114	-0.1215	0.0172	0.0429	0.3977	0.0687	0.0295	0.5367	0.015	0.0373	-35.232	8.736	3.917

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 70
2	X-RAY DIFFRACTION	2	A	71 - 189
3	X-RAY DIFFRACTION	3	A	190 - 200
4	X-RAY DIFFRACTION	4	A	201 - 267
5	X-RAY DIFFRACTION	5	A	268 - 330
6	X-RAY DIFFRACTION	6	A	331 - 405
7	X-RAY DIFFRACTION	7	B	1 - 80
8	X-RAY DIFFRACTION	8	B	81 - 219
9	X-RAY DIFFRACTION	9	B	220 - 278
10	X-RAY DIFFRACTION	10	B	279 - 316
11	X-RAY DIFFRACTION	11	B	317 - 351
12	X-RAY DIFFRACTION	12	B	352 - 405
13	X-RAY DIFFRACTION	13	C	1 - 95
14	X-RAY DIFFRACTION	14	C	96 - 212
15	X-RAY DIFFRACTION	15	C	213 - 278
16	X-RAY DIFFRACTION	16	C	279 - 316
17	X-RAY DIFFRACTION	17	C	317 - 343
18	X-RAY DIFFRACTION	18	C	344 - 405

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