PDB-5tcb: Structure of the glycoside hydrolase domain of PelA from Pseudomo...

ID or keywords:

Entry

Database: PDB / ID: 5tcb

Title

Structure of the glycoside hydrolase domain of PelA from Pseudomonas aeruginosa

Components

PelA

Keywords

HYDROLASE / glycoside hydrolase

Function / homology

Function and homology information

deacetylase activity / : / single-species biofilm formation
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.535 Å

Authors

Alnabelseya, N. / Baker, P. / Robinson, H. / Howell, P.L.

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: Microbial glycoside hydrolases display cross-kingdom activity against bacterial and fungal biofilms
Authors: Snarr, B.D. / Baker, P. / Bamford, N.C. / Sato, Y. / Alnabelseya, N. / Lui, H. / Gravelad, F.N. / Ostapska, H. / Baistrocchi, S.R. / Cerone, R.P. / Robinson, H. / Filler, S.G. / Howell, P.L. / Sheppard, D.C.

History

Deposition	Sep 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5tcb.cif.gz	154.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5tcb.ent.gz	123.7 KB	Display	PDB format
PDBx/mmJSON format	5tcb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5tcb_validation.pdf.gz	420.6 KB	Display	wwPDB validaton report
Full document	5tcb_full_validation.pdf.gz	421.6 KB	Display
Data in XML	5tcb_validation.xml.gz	12.6 KB	Display
Data in CIF	5tcb_validation.cif.gz	18.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/5tcb ftp://data.pdbj.org/pub/pdb/validation_reports/tc/5tcb	HTTPS FTP

-
Related structure data

Related structure data	5tsyC C: citing same article (ref.)
Similar structure data	5tsy-d 3sfm-1 5ynu-2 4pne-2 1vpq-d 6uba-9 5jnc-3 2vfb-d 6uba-2 4nv8-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: PelA

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	64.983, 84.031, 47.177
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

Monomer confirmed by Size Exclusion Chromatography

#1: Protein	PelA Mass: 30575.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: pelA, PA3064 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZE4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

PelA

Mass: 30575.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pelA, PA3064 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZE4

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.11	41.61
2	2.11	41.61

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion, hanging drop	7.5	25% (w/v) PEG 5000 MME, 100 mM Bis-Tris pH 7.5
293	2	vapor diffusion, hanging drop	7.5	26% (w/v) PEG 5000 MME, 100 mM Bis-Tris pH 7.5

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	93	1
2	93	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X29A	1	1.075
SYNCHROTRON	NSLS	X29A	2	0.9792

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	Jan 11, 2013
ADSC QUANTUM 315r	2	CCD	Jan 11, 2013

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.075	1
2	0.9792	1

Reflection

Entry-ID: 5TCB

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Net I/σ(I)
1.53-50	39286	99.9	17	0.181	1	18.6
1.9-50	19863	99.8	15.4	0.122	2	21.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.53-1.58	13.7	0.443	6.6	1	99.5
1.9-1.97	13.4	0.625	4.5	2	99.7

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.535→50 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.06

	R_factor	Num. reflection	% reflection
R_free	0.1917	3772	5.08 %
R_work	0.1687	-	-
obs	0.1699	39193	99.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.535→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1918	0	0	193	2111

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1983
X-RAY DIFFRACTION	f_angle_d	0.935	2704
X-RAY DIFFRACTION	f_dihedral_angle_d	13.623	1177
X-RAY DIFFRACTION	f_chiral_restr	0.055	289
X-RAY DIFFRACTION	f_plane_restr	0.007	361

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 (%)
1.535-1.5544	0.2426	126	0.2043	2382	X-RAY DIFFRACTION	90
1.5544-1.5749	0.2254	141	0.199	2646	X-RAY DIFFRACTION	100
1.5749-1.5964	0.2379	139	0.1982	2566	X-RAY DIFFRACTION	100
1.5964-1.6192	0.2823	135	0.1891	2627	X-RAY DIFFRACTION	100
1.6192-1.6434	0.2095	136	0.1785	2618	X-RAY DIFFRACTION	100
1.6434-1.6691	0.1917	144	0.1786	2659	X-RAY DIFFRACTION	100
1.6691-1.6965	0.1884	130	0.1749	2571	X-RAY DIFFRACTION	100
1.6965-1.7257	0.1968	144	0.1765	2622	X-RAY DIFFRACTION	100
1.7257-1.7571	0.2521	145	0.1806	2656	X-RAY DIFFRACTION	100
1.7571-1.7909	0.2209	139	0.1749	2618	X-RAY DIFFRACTION	100
1.7909-1.8274	0.1993	144	0.1882	2597	X-RAY DIFFRACTION	100
1.8274-1.8672	0.2046	140	0.1835	2656	X-RAY DIFFRACTION	100
1.8672-1.9106	0.2113	137	0.1763	2627	X-RAY DIFFRACTION	100
1.9106-1.9584	0.1906	139	0.1612	2612	X-RAY DIFFRACTION	100
1.9584-2.0113	0.2202	140	0.1687	2622	X-RAY DIFFRACTION	100
2.0113-2.0705	0.2239	141	0.1714	2612	X-RAY DIFFRACTION	100
2.0705-2.1373	0.1795	135	0.1669	2621	X-RAY DIFFRACTION	100
2.1373-2.2137	0.2426	140	0.1729	2628	X-RAY DIFFRACTION	100
2.2137-2.3023	0.1555	144	0.1731	2621	X-RAY DIFFRACTION	100
2.3023-2.4071	0.2043	141	0.162	2643	X-RAY DIFFRACTION	100
2.4071-2.534	0.2018	140	0.1699	2613	X-RAY DIFFRACTION	100
2.534-2.6927	0.2077	137	0.182	2615	X-RAY DIFFRACTION	100
2.6927-2.9006	0.1684	143	0.1745	2638	X-RAY DIFFRACTION	100
2.9006-3.1923	0.2248	139	0.1762	2606	X-RAY DIFFRACTION	100
3.1923-3.6539	0.1778	142	0.1709	2631	X-RAY DIFFRACTION	100
3.6539-4.6023	0.1466	144	0.1463	2616	X-RAY DIFFRACTION	100
4.6023-38.1888	0.1886	147	0.1569	2612	X-RAY DIFFRACTION	100

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	1.0254	-0.1447	0.9093	1.6402	0.1246	7.3421	0.0992	-0.0308	-0.1081	-0.1448	-0.0006	0.1037	0.284	-0.0681	-0.0637	0.1419	-0.0198	-0.0048	0.1371	-0.0041	0.179	45.8916	18.1509	1.0939
2	9.8697	1.2906	-3.4736	2.8742	1.8676	3.2906	0.1875	-0.2457	-0.6809	0.6011	-0.1447	0.1071	1.5703	-0.6883	-0.3051	0.7448	-0.1377	0.096	0.3186	0.0988	0.4357	45.3874	8.504	25.8956
3	1.9754	3.3341	0.3774	7.9751	0.4106	6.6923	-0.2235	-0.3214	0.1576	0.522	-0.0356	0.8348	-0.2275	-0.7093	0.2763	0.2328	0.032	0.0482	0.3342	-0.0274	0.2032	44.5645	19.1938	26.6852
4	0.7363	-0.2348	-0.4506	1.7812	1.0407	3.9236	-0.0405	-0.1051	-0.0614	0.0395	0.111	0.0272	0.1498	0.1085	-0.0314	0.1365	-0.024	-0.0039	0.2002	0.0017	0.1834	52.7218	16.8833	15.2676
5	2.5625	-1.2064	-2.9981	3.065	3.4817	8.058	0.0536	-0.1239	-0.0201	0.1055	0.148	-0.1702	0.0926	0.4657	-0.2852	0.1514	-0.0138	-0.0083	0.2602	-0.0237	0.1785	58.9172	23.0329	22.8544
6	1.575	-0.3587	1.1797	2.7895	1.0806	3.7697	-0.0905	-0.2807	0.1659	-0.0227	-0.0159	0.0737	-0.3178	-0.3441	0.0439	0.1448	-0.0243	0.0211	0.1959	-0.0306	0.1352	49.0351	30.5164	11.9359
7	9.0055	-2.0414	-5.1869	4.7982	2.033	3.5254	-0.1604	0.3568	0.7888	-0.0004	0.1397	-0.038	-0.7565	0.0295	-0.0208	0.4577	-0.0824	-0.1041	0.2467	0.0128	0.4151	51.0257	41.6861	13.4589
8	1.6015	1.1661	1.7507	2.1798	0.6458	2.3411	-0.5839	-0.296	0.576	-0.4039	0.0457	0.161	-0.7698	-0.2509	0.3721	0.3529	0.0581	-0.0789	0.1842	-0.0484	0.2036	39.7452	35.8578	1.0976
9	8.2022	2.6359	1.655	4.0657	0.8812	2.5082	-0.3554	0.0141	0.2757	-0.3159	0.1798	0.2596	-0.5102	-0.211	0.264	0.2363	0.0198	-0.0274	0.1571	-0.0007	0.1484	40.5898	31.0945	0.2465

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 48 through 105 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 106 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 135 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 136 through 169 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 170 through 190 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 235 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 236 through 252 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 253 through 279 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 280 through 300 )

-
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