PDB-5o78: Crystal structure of Omp35 from Enterobacter aerogenes

ID or keywords:

Entry

Database: PDB / ID: 5o78

Title

Crystal structure of Omp35 from Enterobacter aerogenes

Components

Phosphoporin PhoE

Keywords

MEMBRANE PROTEIN / Outer membrane / trimer / porin / passive diffusion

Function / homology

Function and homology information

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

Biological species

Enterobacter aerogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Ferrara, L. / Naismith, J.

Citation

Journal: To Be Published
Title: Crystal structure of Omp35 from Enterobacter aerogenes
Authors: Ferrara, L. / Naismith, J.

History

Deposition	Jun 8, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 20, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 / _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	5o78.cif.gz	386 KB	Display	PDBx/mmCIF format
PDB format	pdb5o78.ent.gz	323.1 KB	Display	PDB format
PDBx/mmJSON format	5o78.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5o78_validation.pdf.gz	439.6 KB	Display	wwPDB validaton report
Full document	5o78_full_validation.pdf.gz	447.3 KB	Display
Data in XML	5o78_validation.xml.gz	33.4 KB	Display
Data in CIF	5o78_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o7/5o78 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o78	HTTPS FTP

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Related structure data

Related structure data	1omf PDB Unreleased entryS S: Starting model for refinement
Similar structure data	6rcp-1 6zhv-d 3hw9-1 5o77-1 4gcp-1 3k19-1 4d5u-2 1gfo-1 4jfb-1 4gcq-2 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: Phosphoporin PhoE

B: Phosphoporin PhoE

C: Phosphoporin PhoE

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

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	111.570, 115.940, 216.661
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

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: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 7 - 337 / Label seq-ID: 7 - 337

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	Phosphoporin PhoE Mass: 37359.344 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ASV18_23685, BXQ27_19200 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A0F1QVM5, UniProt: A0A0H3FYJ7*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.19 Å³/Da / Density % sol: 61.41 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium Chloride, 0.05 M magnesium sulfate, 8% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.85→108.33 Å / Num. obs: 27313 / % possible obs: 85 % / Redundancy: 2.5 % / CC_1/2: 0.99 / R_merge(I) obs: 0.11 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.85→2.92 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
Coot		model building
SCALA		data scaling
MOLREP		phasing
MOSFLM		data processing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1omf

1omf
PDB Unreleased entry

Resolution: 2.85→108.33 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.862 / SU B: 39.607 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26034	1375	5 %	RANDOM
R_work	0.2136	-	-	-
obs	0.21597	25937	82.21 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å

Displacement parameters

B_iso mean: 54.818 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.55 Å²	0 Å²	0 Å²
2-	-	-2.44 Å²	0 Å²
3-	-	-	-0.1 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→108.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7764	0	0	1	7765

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	7940
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6625
X-RAY DIFFRACTION	r_angle_refined_deg	1.462	1.908	10747
X-RAY DIFFRACTION	r_angle_other_deg	0.915	3	15350
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.274	5	990
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.043	24.933	450
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.562	15	1182
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.576	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	1071
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9362
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1822
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	2.351	2.949	3969
X-RAY DIFFRACTION	r_mcbond_other	2.349	2.949	3968
X-RAY DIFFRACTION	r_mcangle_it	3.843	4.424	4956
X-RAY DIFFRACTION	r_mcangle_other	3.843	4.424	4957
X-RAY DIFFRACTION	r_scbond_it	2.867	3.206	3971
X-RAY DIFFRACTION	r_scbond_other	2.867	3.206	3972
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.682	4.707	5792
X-RAY DIFFRACTION	r_long_range_B_refined	6.702	33.828	8618
X-RAY DIFFRACTION	r_long_range_B_other	6.702	33.828	8619
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	20420	0.09
1	2	B	20420	0.09
2	1	A	20328	0.1
2	2	C	20328	0.1
3	1	B	20392	0.1
3	2	C	20392	0.1

LS refinement shell

Resolution: 2.85→2.924 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	91	-
R_work	0.335	1964	-
obs	-	-	84.57 %

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	1.3584	0.2961	0.8233	0.0958	0.405	2.438	0.0808	0.1001	-0.0169	0.0525	-0.0034	-0.0191	0.2608	0.1631	-0.0774	0.1796	0.0126	-0.0162	0.3062	0.0396	0.2601	-28.372	28.726	30.083
2	0.8014	-0.153	-0.2981	0.1312	0.2986	2.5323	0.1738	0.1837	-0.0476	-0.0234	-0.0978	-0.0604	0.1611	0.3215	-0.076	0.1014	0.0136	-0.0253	0.5297	0.0453	0.2768	-20.696	29.554	14.895
3	1.6008	1.4385	-1.4263	4.8986	2.4061	5.6698	0.0002	0.3292	0.183	-0.1194	-0.0174	0.4573	-0.2218	-0.1946	0.0172	0.1571	-0.0353	-0.0247	0.4068	0.017	0.263	-29.87	44.614	13.871
4	2.5105	-1.7338	1.0039	3.9659	-0.8859	2.1164	-0.0299	0.4047	0.1949	-0.3303	-0.0882	-0.2711	-0.0574	0.2463	0.1181	0.0649	-0.0738	0.0479	0.5125	0.1018	0.1666	-13.483	38.92	13.837
5	0.2949	-0.1928	0.5784	0.5228	-0.5586	2.0781	-0.0632	0.2377	0.0559	0.1698	-0.0046	-0.0605	-0.2599	0.2233	0.0678	0.076	-0.0339	-0.0095	0.4407	0.0864	0.282	-9.296	38.87	31.418
6	0.3839	-0.4198	0.7359	3.344	-4.0777	6.3326	-0.1334	0.0871	-0.0473	0.1176	0.0749	-0.0264	-0.1584	-0.055	0.0585	0.1461	0.0137	-0.0279	0.3032	-0.029	0.3033	-42.863	29.772	20.134
7	0.5882	0.0264	0.2437	0.1706	-0.4331	1.3879	-0.0075	0.0463	-0.0471	-0.0874	0.1529	0.0339	0.2204	-0.1933	-0.1454	0.0944	-0.0413	-0.0404	0.4464	0.0728	0.3176	-55.643	26.52	31.164
8	1.0066	0.7169	0.205	4.3614	1.5717	3.8191	-0.0283	-0.0759	0.0109	0.2849	0.1857	0.3497	-0.1088	-0.2034	-0.1574	0.0432	0.0326	0.017	0.4446	0.1501	0.2707	-66.787	36.246	30.41
9	0.6625	-0.3033	-0.6031	0.2317	0.3557	2.3277	0.1063	-0.1565	0.0049	-0.1029	0.2282	0.0424	0.0259	-0.1117	-0.3345	0.1271	-0.0938	-0.0897	0.4207	0.1077	0.3052	-63.933	31.86	15.181
10	1.992	-1.8208	0.0711	2.4223	-0.708	1.1034	-0.0252	0.0128	0.0254	-0.0069	0.2234	0.0971	-0.0021	-0.0506	-0.1982	0.152	-0.0366	-0.0658	0.3231	0.0494	0.2494	-54.561	36.04	10.449
11	4.1931	-1.9053	-0.2567	2.1103	0.7566	0.9534	0.2287	-0.0946	-0.3239	-0.4276	-0.0188	0.0267	-0.252	-0.0447	-0.2099	0.1707	-0.0317	-0.0078	0.2995	0.0769	0.2451	-44.915	29.007	45.465
12	0.4893	-0.1178	0.3783	0.2205	-0.0153	1.2727	-0.0593	-0.2414	-0.1014	-0.0581	0.0154	-0.0166	-0.1172	0.0193	0.0439	0.0487	-0.0089	0.0021	0.4076	0.0244	0.3404	-30.874	30.038	52.735
13	2.5995	0.739	-0.9957	3.2874	-1.5966	2.2246	0.204	-0.1901	-0.0746	0.0454	-0.2866	-0.1707	-0.3669	0.3837	0.0825	0.0955	-0.0076	-0.0106	0.3201	-0.0343	0.2273	-27.42	38.207	59.717
14	2.2491	1.2753	-1.2025	1.0064	-1.0609	1.2316	-0.045	-0.165	0.0713	0.0184	0.0349	-0.0075	-0.1419	0.0421	0.0101	0.2346	-0.0249	0.0089	0.4069	-0.0388	0.2369	-37.552	40.497	64.718
15	0.4245	-0.0308	0.2401	1.904	0.5887	1.9976	-0.0046	-0.1245	0.0246	-0.0158	0.0869	-0.0888	-0.2276	-0.1727	-0.0823	0.0741	0.0267	0.0294	0.3974	0.0618	0.2843	-50.775	38.342	59.549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 81
2	X-RAY DIFFRACTION	2	A	82 - 150
3	X-RAY DIFFRACTION	3	A	151 - 169
4	X-RAY DIFFRACTION	4	A	170 - 246
5	X-RAY DIFFRACTION	5	A	247 - 337
6	X-RAY DIFFRACTION	6	B	7 - 37
7	X-RAY DIFFRACTION	7	B	38 - 143
8	X-RAY DIFFRACTION	8	B	144 - 211
9	X-RAY DIFFRACTION	9	B	212 - 255
10	X-RAY DIFFRACTION	10	B	256 - 337
11	X-RAY DIFFRACTION	11	C	7 - 44
12	X-RAY DIFFRACTION	12	C	45 - 145
13	X-RAY DIFFRACTION	13	C	146 - 193
14	X-RAY DIFFRACTION	14	C	194 - 254
15	X-RAY DIFFRACTION	15	C	255 - 337

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