PDB-3t24: Crystal structure of Pseudomonas aeruginosa OpdQ

ID or keywords:

Entry

Database: PDB / ID: 3t24

Title

Crystal structure of Pseudomonas aeruginosa OpdQ

Components

porin

Keywords

MEMBRANE PROTEIN /

beta-barrel / channel /

bacterial outer membrane

Function / homology

Function and homology information

response to nitrate / cellular response to oxygen levels / channel activity /

porin activity / membrane => GO:0016020
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

van den Berg, B. / Eren, E.

Citation

Journal: Plos Biol. / Year: 2012
Title: Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
Authors: Eren, E. / Vijayaraghavan, J. / Liu, J. / Cheneke, B.R. / Touw, D.S. / Lepore, B.W. / Indic, M. / Movileanu, L. / van den Berg, B.

History

Deposition	Jul 22, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3t24.cif.gz	454.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3t24.ent.gz	375.7 KB	Display	PDB format
PDBx/mmJSON format	3t24.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t2/3t24 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/3t24	HTTPS FTP

-
Related structure data

Related structure data	3sy7C 3sy9C 3sybC 3sysC 3szdC 3szvC 3t0sC 3t20C 2qtkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4frt-1 2y0h-d 4fms-2 4frt-2 2y0k-d 4frx-2 3rbh-1 2y0l-d 4frx-1 3jty-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: porin

B: porin

C: porin

hetero molecules

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

1

A: porin

hetero molecules

defined by author
47.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: porin

hetero molecules

defined by author
46.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: porin

hetero molecules

defined by author
45.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

A: porin

hetero molecules

B: porin

C: porin

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.722, 78.464, 97.519
Angle α, β, γ (deg.)	77.76, 81.50, 70.04
Int Tables number	1
Space group name H-M	P1

#1: Protein	porin / Mass: 45016.980 Da / Num. of mol.: 3 / Fragment: unp residues 28-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3038 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZH0
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.59 %
Crystal grow	Temperature: 295 K / pH: 5.5 Details: 33% PEG 1K 0.2 M ammonium sulphate 50 mM Na-acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2011
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972 Å / Relative weight: 1
Reflection	Resolution: 2.35→50 Å / Num. obs: 67240 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / R_sym value: 0.084 / Net I/σ(I): 17.7
Reflection shell	Resolution: 2.35→2.39 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.8 / R_sym value: 0.494 / % possible all: 97.3

-
Processing

Software

Name	Version	Classification
CBASS		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2QTK

2qtk

Resolution: 2.4→14.98 Å / SU ML: 0.77 / σ(F): 1.97 / Phase error: 23.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.242	1974	2.94 %
R_work	0.203	-	-
obs	0.204	67240	98.3 %
all	-	67240	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 62.66 Å² / k_sol: 0.36 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.0357 Å²	-1.9077 Å²	3.7043 Å²
2-	-	0.5829 Å²	-0.3877 Å²
3-	-	-	4.4528 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→14.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8578	0	234	238	9050

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8967
X-RAY DIFFRACTION	f_angle_d	1.091	12061
X-RAY DIFFRACTION	f_dihedral_angle_d	17.001	3246
X-RAY DIFFRACTION	f_chiral_restr	0.075	1242
X-RAY DIFFRACTION	f_plane_restr	0.004	1555

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.4598	0.3569	139	0.3173	4590	X-RAY DIFFRACTION	98
2.4598-2.526	0.3417	140	0.2864	4635	X-RAY DIFFRACTION	98
2.526-2.5999	0.3331	141	0.2536	4666	X-RAY DIFFRACTION	98
2.5999-2.6834	0.2753	141	0.232	4636	X-RAY DIFFRACTION	98
2.6834-2.7787	0.2549	140	0.211	4657	X-RAY DIFFRACTION	98
2.7787-2.8892	0.2381	140	0.2012	4620	X-RAY DIFFRACTION	98
2.8892-3.0197	0.27	141	0.2023	4693	X-RAY DIFFRACTION	98
3.0197-3.1775	0.2537	141	0.2032	4651	X-RAY DIFFRACTION	99
3.1775-3.3744	0.234	142	0.1947	4689	X-RAY DIFFRACTION	99
3.3744-3.6315	0.227	142	0.1913	4673	X-RAY DIFFRACTION	99
3.6315-3.9907	0.2073	141	0.1937	4670	X-RAY DIFFRACTION	99
3.9907-4.5539	0.2042	142	0.1809	4714	X-RAY DIFFRACTION	99
4.5539-5.6849	0.2467	142	0.1836	4696	X-RAY DIFFRACTION	99
5.6849-14.9847	0.2419	142	0.2138	4676	X-RAY DIFFRACTION	99

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	8.7496	-3.134	-1.491	2.7255	0.7542	1.2894	0.3172	0.7158	-0.7609	-0.2033	-0.3658	0.5048	-0.0073	-0.093	0.0301	0.3408	-0.0433	-0.0752	0.3731	-0.0109	0.2441	-9.032	-9.1052	-34.3847
2	1.0751	0.1891	-0.7272	0.9624	-0.0166	1.3556	-0.1137	0.0857	-0.2616	0.1255	0.1257	0.4472	0.1273	-0.1142	-0.044	0.2111	-0.0267	-0.024	0.2719	0.0248	0.4524	-13.3793	-5.0985	-25.157
3	2.0256	-1.1949	-0.3031	5.5275	-0.4625	1.5439	0.1273	0.1121	-0.1482	0.0818	-0.0133	0.9154	-0.0604	-0.111	-0.095	0.1616	-0.0213	0.0344	0.2155	0.0044	0.3895	-8.0121	6.3401	-24.9361
4	4.4915	-0.6185	0.2019	1.8757	1.3359	3.9565	-0.0463	-0.0524	-1.2116	0.5634	-0.0184	0.2278	0.3985	-0.4548	0.0542	0.3254	-0.0015	0.0494	0.2262	0.071	0.4175	5.3376	-3.0957	-22.6263
5	4.5076	-2.9773	-0.8038	5.9356	-1.3404	2.6778	0.0304	-0.1045	0.3875	0.2262	0.2841	0.4062	-0.1655	-0.4023	-0.2716	0.1536	-0.0626	0.0502	0.1601	-0.0704	0.3411	-0.7772	12.319	-24.0375
6	3.0867	0.0493	-0.3935	2.0819	0.0284	1.7545	0.1313	0.8586	0.4938	-0.3088	-0.0121	0.1453	-0.1239	-0.2744	-0.0619	0.2348	0.0635	0.0152	0.4497	0.1178	0.2897	3.4804	6.587	-39.6079
7	2.1325	0.7816	-1.1325	1.4827	-0.0522	0.6638	0.4092	0.9454	-0.2442	-0.1625	-0.1533	0.2016	0.0327	-0.2471	-0.2727	0.2776	0.01	-0.0513	0.4742	-0.0498	0.3215	-0.1665	-9.1306	-40.4741
8	2.1511	-1.1168	-3.9145	2.9429	0.5257	4.648	-0.4392	0.0934	-0.4445	0.2288	0.0591	-0.4105	0.5842	-0.1478	0.3482	0.5055	-0.038	-0.146	0.2979	-0.0088	0.7028	21.3672	-41.5815	-18.1604
9	-0.0783	0.157	0.1672	1.8398	0.5991	0.9912	-0.0781	-0.2903	-1.2592	0.0369	0.0299	-0.3965	0.2901	-0.0121	0.025	0.3519	0.0019	0.0369	0.2768	0.0189	0.9104	32.7386	-32.0196	-24.8803
10	5.1537	-0.1083	-0.3524	1.466	0.7876	1.7117	0.1179	-0.1339	-1.0329	-0.0242	-0.1193	-0.2491	0.2903	-0.0344	-0.0428	0.2894	-0.0346	0.0564	0.1603	0.0767	0.4932	28.1059	-19.7284	-21.9983
11	1.9936	0.7381	-0.3843	3.3911	-0.3079	2.3916	0.1793	-0.6002	-0.1382	0.5112	-0.2203	-0.3698	0.0625	0.1589	0.0496	0.2722	-0.0845	-0.0252	0.3481	0.0325	0.2311	25.4142	-16.0162	-8.0307
12	3.0995	-1.5846	0.4512	6.2018	-1.1846	2.7288	0.0989	-0.6526	-0.7598	0.7967	-0.0227	0.4159	0.3995	-0.0969	-0.0514	0.4713	-0.1322	0.0031	0.433	0.1335	0.3823	17.8464	-29.1655	-2.7792
13	0.1735	-0.4582	0.4415	4.3883	0.6201	1.3113	0.4494	-0.238	-0.6709	0.1961	-0.2733	0.3142	0.2152	0.0339	-0.2457	0.4985	-0.0822	-0.0542	0.3964	0.1288	0.7299	16.4271	-37.0756	-9.6308
14	1.4083	0.3293	-0.1476	1.2559	-1.4418	6.3327	0.4343	-0.4316	0.2739	-0.3505	-0.0818	0.0465	-0.8149	-0.0514	-0.2827	1.2593	-0.1177	0.292	0.5936	-0.0545	0.7289	36.3935	20.5828	17.1458
15	-0.032	0.08	-0.687	-0.1805	-0.7288	6.1838	-0.0147	-0.3348	0.0328	0.2026	0.1234	-0.1197	-1.5977	0.8894	-0.0581	0.7158	-0.1692	-0.0326	0.6112	0.0238	0.5482	39.4238	15.3227	8.7359
16	3.8278	1.5221	-0.3754	3.0868	0.1859	3.4264	-0.2654	-0.0058	0.1832	0.0584	0.1884	-0.1338	-0.647	0.9379	0.0442	0.5858	-0.0904	0.0045	0.5349	0.0348	0.2692	37.0754	4.9078	8.7994
17	2.4051	0.1527	0.0001	2.7527	-0.543	8.9936	-0.286	-0.4163	-0.1882	-0.2016	0.0187	-0.3493	0.6919	0.8733	0.2489	0.6879	0.0984	0.0907	0.5922	0.0318	0.2999	36.6724	-2.8346	14.9393
18	4.5188	-0.487	-0.4402	3.2412	-0.2068	8.5948	-0.1862	-0.3446	-0.3102	-0.2038	-0.1328	0.0441	1.1759	-0.3197	0.2126	0.7257	-0.0662	0.0441	0.585	0.0831	0.2329	27.7235	-5.8272	21.0228
19	2.8024	0.1586	-1.209	3.4424	-0.483	6.7052	-0.0965	-0.3678	-0.0612	0.3778	0.0489	0.0524	0.0371	-0.3027	0.0409	0.5438	0.0645	0.0141	0.6189	0.0177	0.2092	28.4016	1.7669	29.4125
20	4.2303	-2.0976	0.7559	5.3003	-2.7441	5.5682	0.1986	-0.3631	0.5808	0.3346	0.5867	0.5913	-1.0301	-0.5306	-0.6717	0.9827	0.1623	0.1277	0.6456	-0.1604	0.4602	25.083	17.2112	28.7486
21	1.4981	0.1464	-0.4852	5.6582	-5.5737	6.1256	0.2643	-0.2361	0.4613	0.0482	-0.0749	-0.1171	-0.914	0.5791	-0.2323	1.0079	-0.0315	0.088	0.6114	-0.1352	0.4589	33.5247	15.8677	29.0802

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -1:25)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 26:111)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 112:154)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 155:174)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 175:197)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 198:363)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 364:394)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 3:44)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 45:128)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 129:197)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 198:283)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 284:363)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 364:394)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 0:22)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 23:111)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 112:154)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 155:225)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 226:260)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 261:343)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 344:362)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 363:394)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi