PDB-6au1: Structure of the PgaB (BpsB) glycoside hydrolase domain from Bord...

ID or keywords:

Entry

Database: PDB / ID: 6au1

Title

Structure of the PgaB (BpsB) glycoside hydrolase domain from Bordetella bronchiseptica

Components

Putative hemin storage protein

Keywords

HYDROLASE /

deacetylase /

glycoside hydrolase / PNAG /

biofilm

Function / homology

Function and homology information

cell adhesion involved in biofilm formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process
Similarity search - Function

Biological species

Bordetella bronchiseptica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Little, D.J. / Bamford, N.C. / Howell, P.L.

Funding support

Canada, 1items

Citation

Journal: PLoS Pathog. / Year: 2018
Title: PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-beta (1,6)-N-acetylglucosamine and can disrupt bacterial biofilms.
Authors: Little, D.J. / Pfoh, R. / Le Mauff, F. / Bamford, N.C. / Notte, C. / Baker, P. / Guragain, M. / Robinson, H. / Pier, G.B. / Nitz, M. / Deora, R. / Sheppard, D.C. / Howell, P.L.

History

Deposition	Aug 30, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 16, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6au1.cif.gz	304.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6au1.ent.gz	245.6 KB	Display	PDB format
PDBx/mmJSON format	6au1.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/au/6au1 ftp://data.pdbj.org/pub/pdb/validation_reports/au/6au1	HTTPS FTP

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Related structure data

Related structure data	4p7lS S: Starting model for refinement
Similar structure data	6p3m-d 4moc-d 5u5k-d 3q1c-d 4qmp-d 1wc6-2 6l0r-1 4naj-d 6sfb-1 6p3o-d 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

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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: Putative hemin storage protein

B: Putative hemin storage protein

hetero molecules

82.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative hemin storage protein

hetero molecules

defined by author
Evidence: gel filtration, Monomer by size exclusion chromatography
41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative hemin storage protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.102, 91.649, 75.295
Angle α, β, γ (deg.)	90.00, 111.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative hemin storage protein / PgaB (BpsB / HmsF) / Poly-beta-1 / 6-N-acetyl-D-glucosamine hydrolase Mass: 40527.977 Da / Num. of mol.: 2 / Fragment: UNP residues 318-670 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: hmsF, BB1768, PgaB (BpsB,HmsF) / Plasmid: pET28a / Production host: Escherichia coli BL21 (DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: A0A0H3LKK6, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.88 Å³/Da / Density % sol: 57.36 % / Description: Large rectangles
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.1 M BIS-TRIS pH 6.9, 0.2 M lithium sulfate, and 1.7 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. obs: 177772 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / R_merge(I) obs: 0.062 / Net I/σ(I): 36.6
Reflection shell	Resolution: 1.76→1.82 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.249 / Mean I/σ(I) obs: 7.9 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
PHENIX	dev_1760	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4P7L

4p7l

Resolution: 1.76→45.825 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.9

	R_factor	Num. reflection	% reflection
R_free	0.1671	3934	2.21 %
R_work	0.1511	-	-
obs	0.1515	177772	99.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.76→45.825 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5630	0	57	510	6197

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5858
X-RAY DIFFRACTION	f_angle_d	1.069	7983
X-RAY DIFFRACTION	f_dihedral_angle_d	12.51	2183
X-RAY DIFFRACTION	f_chiral_restr	0.047	844
X-RAY DIFFRACTION	f_plane_restr	0.005	1052

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 (%)
1.7573-1.7788	0.274	127	0.2046	5419	X-RAY DIFFRACTION	88
1.7788-1.8013	0.1965	147	0.1843	6321	X-RAY DIFFRACTION	100
1.8013-1.825	0.2109	140	0.1667	6190	X-RAY DIFFRACTION	100
1.825-1.85	0.1673	125	0.1606	6315	X-RAY DIFFRACTION	100
1.85-1.8764	0.1716	146	0.159	6236	X-RAY DIFFRACTION	100
1.8764-1.9044	0.1767	143	0.1539	6200	X-RAY DIFFRACTION	100
1.9044-1.9342	0.2167	144	0.1499	6256	X-RAY DIFFRACTION	100
1.9342-1.9659	0.1528	129	0.1446	6242	X-RAY DIFFRACTION	100
1.9659-1.9998	0.1886	160	0.1527	6188	X-RAY DIFFRACTION	100
1.9998-2.0362	0.1698	127	0.1462	6281	X-RAY DIFFRACTION	100
2.0362-2.0753	0.1693	139	0.1451	6226	X-RAY DIFFRACTION	100
2.0753-2.1177	0.1728	155	0.1461	6260	X-RAY DIFFRACTION	100
2.1177-2.1637	0.1565	129	0.1421	6220	X-RAY DIFFRACTION	100
2.1637-2.2141	0.1823	139	0.1482	6270	X-RAY DIFFRACTION	100
2.2141-2.2694	0.184	140	0.1555	6175	X-RAY DIFFRACTION	100
2.2694-2.3308	0.1845	158	0.1592	6258	X-RAY DIFFRACTION	100
2.3308-2.3994	0.1435	146	0.1501	6202	X-RAY DIFFRACTION	100
2.3994-2.4768	0.1749	132	0.1525	6326	X-RAY DIFFRACTION	100
2.4768-2.5653	0.1912	140	0.159	6180	X-RAY DIFFRACTION	100
2.5653-2.668	0.2008	135	0.1594	6255	X-RAY DIFFRACTION	100
2.668-2.7894	0.1865	147	0.1596	6208	X-RAY DIFFRACTION	100
2.7894-2.9365	0.1607	142	0.1538	6212	X-RAY DIFFRACTION	100
2.9365-3.1204	0.1498	135	0.1596	6248	X-RAY DIFFRACTION	100
3.1204-3.3613	0.1482	141	0.1579	6208	X-RAY DIFFRACTION	100
3.3613-3.6994	0.1712	144	0.1484	6217	X-RAY DIFFRACTION	100
3.6994-4.2344	0.1499	144	0.1377	6258	X-RAY DIFFRACTION	100
4.2344-5.3336	0.1356	140	0.1351	6243	X-RAY DIFFRACTION	100
5.3336-45.8401	0.16	140	0.1503	6224	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	5.397	-1.3136	4.1969	3.0382	-1.3248	6.9825	-0.006	-0.0398	0.2845	-0.0389	-0.0483	-0.042	-0.2954	0.1527	0.0708	0.1004	0.0094	0.0614	0.1187	-0.0277	0.1181	88.4503	13.2814	20.1937
2	0.726	0.4321	0.1665	2.0683	0.6934	0.9486	0.0367	-0.0663	0.0054	0.0627	-0.0839	0.0731	0.0391	-0.0897	0.0489	0.1101	0.0187	-0.0022	0.1553	-0.021	0.1189	76.4687	-5.8406	23.7471
3	2.0412	0.6536	-0.1811	8.1103	4.344	4.5286	0.0145	-0.0667	0.1526	-0.2657	-0.2732	0.55	-0.1719	-0.3935	0.3081	0.067	0.0228	-0.0282	0.1933	-0.0146	0.2015	64.2924	-8.2618	17.8995
4	2.9563	0.4089	-0.0378	3.0121	-1.051	3.2379	-0.0484	-0.0753	0.1627	-0.141	-0.0003	0.3742	-0.1036	-0.3014	0.0419	0.1244	0.0344	-0.0727	0.1589	-0.0328	0.1854	69.5881	-2.8595	10.7229
5	7.3644	-0.097	-2.7807	1.9672	0.0882	5.7667	-0.0659	0.4209	-0.0981	-0.6439	-0.0365	0.0428	0.2166	0.1396	0.0663	0.3103	0.0577	-0.0657	0.1191	-0.0259	0.1566	77.3677	0.4289	0.2559
6	6.3133	0.7216	1.2895	2.5457	-0.5316	3.9228	0.1117	0.288	-0.0895	-0.4352	-0.1309	-0.0113	0.0772	0.1642	0.0187	0.2173	0.0585	-0.0288	0.1228	-0.0095	0.1173	82.047	6.8736	2.4355
7	4.9965	0.4763	1.9238	4.3447	-1.083	6.1906	-0.1939	0.0957	0.625	-0.094	-0.045	-0.0424	-0.5948	0.1939	0.2182	0.2203	0.0307	0.0139	0.1424	0.0016	0.1659	84.8344	14.4417	7.8632
8	4.0947	-0.8386	-2.5197	3.2837	0.7798	5.9838	-0.0266	-0.0821	-0.5062	0.0156	-0.1058	0.27	0.2641	-0.2156	0.1534	0.0803	-0.0089	-0.0393	0.131	0.0139	0.1873	92.2403	-36.0234	22.4309
9	0.9761	0.1535	-0.0439	4.127	0.5164	1.9746	0.0223	-0.0757	-0.0767	0.122	0.0031	-0.047	0.0601	0.0162	-0.0268	0.0636	0.0126	-0.0004	0.1173	0.0235	0.1013	99.1656	-26.784	27.0892
10	0.7274	0.2572	-0.0424	2.7443	-1.1529	1.561	0.0312	-0.0429	0.0642	0.1027	-0.1006	-0.1209	-0.1944	0.1119	0.0614	0.1078	-0.0021	-0.0017	0.1193	0.009	0.1086	108.1879	-9.1634	21.2671
11	0.4278	0.455	-0.3362	7.4033	-5.6322	4.2786	-0.0123	-0.1091	-0.084	-0.1801	-0.2957	-0.4544	0.058	0.397	0.4038	0.1168	0.0064	0.0208	0.1775	0.0425	0.1895	116.4103	-14.7339	17.2503
12	2.1029	0.0713	0.198	2.8144	0.0675	3.4082	0.0117	-0.0609	-0.1339	-0.1779	0.0134	-0.2416	0.046	0.2395	-0.0001	0.0925	0.0204	0.0402	0.1347	0.0101	0.1369	110.7661	-20.5635	10.6429
13	6.8833	-0.5919	2.7925	2.3842	-0.2727	5.9291	0.0107	0.321	0.0188	-0.5502	-0.0074	0.025	-0.1877	-0.1925	-0.0231	0.254	0.0257	0.0459	0.079	0.0004	0.1362	103.1442	-24.6013	0.945
14	6.1058	0.1761	-1.8529	3.1242	0.7522	3.8425	0.0097	0.1946	0.0649	-0.3337	-0.0785	0.1433	-0.0675	-0.3468	0.043	0.1796	0.0442	0.0012	0.1284	-0.0092	0.1011	96.9841	-31.0672	3.9601
15	4.6956	0.7551	-3.0863	5.052	1.2608	6.6114	-0.2691	0.0277	-0.4971	-0.137	-0.0791	0.1778	0.7208	-0.2661	0.3248	0.2007	0.0115	-0.0151	0.1612	-0.0061	0.1589	95.254	-38.3364	9.9509

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 318 through 352 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 353 through 507 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 508 through 536 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 537 through 572 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 573 through 603 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 604 through 640 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 641 through 670 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 318 through 352 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 353 through 417 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 418 through 507 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 508 through 536 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 537 through 572 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 573 through 604 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 605 through 640 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 641 through 670 )

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