PDB-3sy9: Crystal structure of Pseudomonas aeruginosa OccD2 (OpdC)

ID or keywords:

Entry

Database: PDB / ID: 3sy9

Title

Crystal structure of Pseudomonas aeruginosa OccD2 (OpdC)

Components

Histidine porin OpdC

Keywords

MEMBRANE PROTEIN /

beta-barrel / channel /

bacterial outer membrane

Function / homology

Function and homology information

channel activity /

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

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 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 16, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3sy9.cif.gz	591.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3sy9.ent.gz	492.4 KB	Display	PDB format
PDBx/mmJSON format	3sy9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sy/3sy9 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/3sy9	HTTPS FTP

-
Related structure data

Related structure data	3sy7C 3sybC 3sysC 3szdC 3szvC 3t0sC 3t20C 3t24C C: citing same article (ref.)
Similar structure data	2y0k-d 5dl5-d 2y0l-d 4fms-2 3sy7-d 5dl8-1 4fsp-d 3syb-d 3szv-d 6cbx-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.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Histidine porin OpdC

B: Histidine porin OpdC

C: Histidine porin OpdC

D: Histidine porin OpdC

hetero molecules

196 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Histidine porin OpdC

hetero molecules

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

2

B: Histidine porin OpdC

hetero molecules

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

3

C: Histidine porin OpdC

hetero molecules

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

4

D: Histidine porin OpdC

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.353, 102.828, 101.696
Angle α, β, γ (deg.)	77.67, 62.57, 62.95
Int Tables number	1
Space group name H-M	P1

#1: Protein

Histidine porin OpdC

Mass: 47525.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria) / Gene: opdC, PA0162 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9I6X0

#2: Chemical

ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE

Mass: 306.438 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM

#3: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside /

Octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H₂O

Sequence details

AUTHORS HAVE STATED THAT THE RESIDUE 328 IS INDEED A VALINE AND NOT A LEUCINE

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.06 Å³/Da / Density % sol: 69.7 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 4000 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.79→50 Å / Num. all: 105852 / Num. obs: 105852 / % possible obs: 83.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.79→2.84 Å / % possible all: 73.6

-
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 / Resolution: 2.8→14.957 Å / SU ML: 0.94 / σ(F): 1.96 / Phase error: 29.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.266	1983	2.77 %	random
R_work	0.2165	-	-	-
obs	0.2179	71573	97.86 %	-
all	-	73322	-	-

Solvent computation

Shrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 57.891 Å² / k_sol: 0.327 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.6604 Å²	-0.8886 Å²	-0.2017 Å²
2-	-	-16.8483 Å²	5.4872 Å²
3-	-	-	10.1879 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→14.957 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11297	0	283	133	11713

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11861
X-RAY DIFFRACTION	f_angle_d	1.296	16032
X-RAY DIFFRACTION	f_dihedral_angle_d	19.557	4132
X-RAY DIFFRACTION	f_chiral_restr	0.101	1655
X-RAY DIFFRACTION	f_plane_restr	0.006	2071

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 (%)
2.8002-2.8698	0.4672	123	0.3531	4558	X-RAY DIFFRACTION	90
2.8698-2.9468	0.382	153	0.3089	5005	X-RAY DIFFRACTION	98
2.9468-3.0328	0.3518	148	0.2956	4942	X-RAY DIFFRACTION	98
3.0328-3.1299	0.3024	134	0.2645	5008	X-RAY DIFFRACTION	98
3.1299-3.2406	0.306	130	0.2376	5013	X-RAY DIFFRACTION	98
3.2406-3.369	0.2793	148	0.2223	4977	X-RAY DIFFRACTION	98
3.369-3.5204	0.2526	140	0.2181	5022	X-RAY DIFFRACTION	98
3.5204-3.7033	0.2787	147	0.1993	5009	X-RAY DIFFRACTION	99
3.7033-3.9314	0.2366	154	0.2165	4978	X-RAY DIFFRACTION	99
3.9314-4.2286	0.2738	150	0.2145	5040	X-RAY DIFFRACTION	99
4.2286-4.6426	0.2173	151	0.1856	4993	X-RAY DIFFRACTION	98
4.6426-5.2882	0.2115	150	0.1792	4964	X-RAY DIFFRACTION	99
5.2882-6.5673	0.2697	122	0.2084	5049	X-RAY DIFFRACTION	99
6.5673-14.9571	0.2766	133	0.2119	5032	X-RAY DIFFRACTION	98

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	0.0678	-0.1327	-0.0558	1.5522	-0.6151	1.4289	-0.1048	0.371	-0.1361	-0.4119	0.375	-0.3763	0.1797	0.2873	-0.2349	0.4865	-0.1087	0.1117	0.5353	-0.0139	0.628	-9.0935	-17.9507	-16.3267
2	2.8553	1.3821	0.3408	4.1502	0.8894	2.8414	-0.2115	0.1347	-0.2485	-0.641	0.0366	-0.1712	0.1005	0.2281	0.1223	0.3208	-0.0514	0.0956	0.3239	0.0009	0.3982	-12.6287	-15.6974	-5.7993
3	2.3416	1.1255	-1.3937	6.9632	1.7894	2.1628	0.1946	0.2277	0.1744	-1.0882	-0.0914	0.1422	-0.1537	-0.1729	0.3119	0.2253	-0.1158	0.0256	0.31	-0.0821	0.4159	-19.72	-16.4664	-0.3661
4	1.2877	-0.8764	0.6728	4.7687	0.1017	1.96	0.114	-0.0795	-0.2312	-0.1374	0.0213	0.0592	0.3596	0.0501	-0.1369	0.3	-0.1024	-0.0192	0.3497	0.0399	0.419	-18.3409	-33.651	3.2284
5	0.3373	-0.3199	-0.6253	3.1369	-0.009	1.7566	-0.1501	0.2178	-0.0822	-0.3988	0.1536	-0.1425	0.2492	0.0042	-0.0283	0.4607	-0.1316	0.0052	0.3415	-0.0298	0.4576	-21.0068	-38.6489	-11.6733
6	0.083	0.453	-0.0473	2.214	-0.1673	1.5707	-0.0486	-0.3788	0.0471	0.4483	0.3055	-0.401	-0.1735	0.2966	-0.2523	0.4745	0.0958	-0.1402	0.5212	0.0002	0.5665	37.4833	-67.1119	34.2444
7	3.1964	-1.3443	-0.3968	4.39	1.4388	0.7785	-0.1016	-0.0113	0.1876	0.7356	0.0008	-0.1232	0.1039	-0.0764	0.0436	0.451	0.0557	-0.1163	0.3636	0.0339	0.4014	33.5107	-71.9817	27.1134
8	3.3689	-1.5181	-1.7756	6.5085	1.3098	8.3641	-0.169	-0.1132	0.2602	1.2196	0.1801	-0.3251	-0.3753	0.6417	-0.0612	0.247	0.0957	-0.0091	0.3687	0.0412	0.357	30.5959	-66.7895	23.9738
9	1.6254	-1.7537	0.237	5.1494	1.1129	2.4246	0.236	-0.3225	0.2776	0.5408	-0.258	-0.3388	-0.2	0.3351	0.3345	0.3135	0.083	-0.1144	0.3181	-0.0582	0.4183	31.9772	-66.3331	15.2018
10	1.6163	0.2562	-0.5812	4.0284	0.2142	2.1491	0.0684	0.0536	0.216	0.0997	0.0631	0.0473	-0.3436	-0.0058	-0.0849	0.2582	0.0818	-0.0107	0.3022	0.0438	0.3496	27.6042	-51.5672	14.84
11	3.3383	0.1318	0.8678	2.3248	-0.0921	1.8937	-0.2487	-0.2318	0.4077	0.1594	0.0723	0.0566	-0.4077	-0.0677	0.1468	0.4837	0.0814	-0.0068	0.2857	-0.0534	0.4975	22.4214	-44.0636	25.4579
12	0.0758	0.4608	0.3211	2.6405	0.2864	1.2271	-0.055	0.1386	0.4779	0.787	0.1303	-0.6116	-0.3142	0.2759	-0.116	0.5698	0.1656	-0.1114	0.4995	-0.0311	0.5572	31.2929	-50.3512	36.2409
13	0.8462	0.0995	0.5062	2.2693	0.5613	2.9401	-0.1825	-0.388	0.2332	0.2754	0.02	0.1169	-0.1929	-0.1164	0.0469	0.2887	0.0349	0.0257	0.2912	0.0041	0.3204	-6.3422	-3.0992	26.1402
14	5.1584	3.1449	0.818	7.669	2.0253	3.946	0.4678	-0.3944	0.2198	0.7348	-0.19	0.0763	-0.3228	-0.0239	-0.2236	0.398	0.0749	0.0215	0.3083	-0.0114	0.3268	-3.5326	-12.6801	28.1213
15	5.0854	-1.4138	1.3446	4.5573	-0.9246	3.7679	0.0831	-0.728	-0.3389	0.3163	0.1112	0.0567	0.3077	-0.3829	-0.0775	0.3455	0.0506	-0.0017	0.3236	0.0989	0.2161	-10.7209	-21.8376	26.5373
16	2.2337	-0.6984	-1.663	1.9331	0.4492	3.8668	-0.0941	-0.4625	-0.1285	0.5929	0.2092	0.2956	0.0675	-0.111	-0.0512	0.6057	0.1434	0.0992	0.5155	0.1113	0.4158	-7.6672	-25.082	41.1611
17	1.4633	-0.6147	-1.0512	2.6823	0.6544	1.1304	-0.2423	-0.431	-0.0189	0.9653	0.2659	-0.0196	0.0932	-0.1989	-0.0852	0.9216	0.2952	0.0411	0.7462	0.0302	0.3468	-0.4013	-19.5329	50.3219
18	1.1143	-1.1914	0.0601	3.1912	-1.7753	2.2568	-0.1613	-0.4335	0.1518	0.65	0.1988	-0.2728	-0.1236	-0.0231	-0.0631	0.7729	0.1456	-0.0824	0.6738	-0.0826	0.3599	-1.9152	-5.2449	46.8832
19	0.4602	-0.2471	-0.13	2.4192	0.6507	2.188	-0.146	0.3556	-0.2453	-0.3849	0.0383	0.0932	0.0866	-0.0817	0.0524	0.3059	-0.0622	-0.0565	0.3089	0.0121	0.3139	-5.9281	-80.7127	81.1965
20	2.184	1.9361	-1.2212	3.6513	-0.024	3.6666	0.4136	0.296	0.2293	-0.4395	-0.1091	-0.417	-0.0643	0.0803	-0.1376	0.3914	-0.1322	0.0335	0.3058	0.057	0.3262	-7.1032	-66.6539	84.0285
21	1.9629	0.3853	1.3449	2.0713	0.1286	4.6452	-0.1118	0.4138	0.1315	-0.599	0.3135	0.2824	-0.2724	-0.3582	-0.0923	0.5553	-0.1233	-0.0948	0.501	0.1463	0.4489	-8.5289	-59.6912	67.9567
22	0.1799	-0.1476	0.5833	1.779	-0.1442	1.8957	-0.2319	0.5438	-0.0154	-0.8846	0.3984	-0.0193	0.154	-0.0925	-0.1011	0.7691	-0.2106	0.0073	0.6867	-0.0124	0.3406	-0.9564	-70.3539	58.9872

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 7:69)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 70:154)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 155:198)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 199:302)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 303:422)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 7:69)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 70:126)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 127:148)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 149:203)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 204:302)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 303:377)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 378:422)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 7:126)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 127:148)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 149:213)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 214:300)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 301:377)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 378:422)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 7:136)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 137:198)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 199:302)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 303:422)

-
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