PDB-6ldd: Structure of Bifidobacterium dentium beta-glucuronidase complexed...

ID or keywords:

Entry

Database: PDB / ID: 6ldd

Title

Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-propyl uronic isofagomine

Components

LacZ1 Beta-galactosidase

Keywords

HYDROLASE / inhibitor / glycosidase / isofagomine

Function / homology

Function and homology information

glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space
Similarity search - Function

Biological species

Bifidobacterium dentium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.205 Å

Authors

Lin, H.-Y. / Hsieh, T.-J. / Lin, C.-H.

Funding support

Taiwan, 1items

Citation

Journal: Commun Biol / Year: 2021
Title: Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.
Authors: Lin, H.Y. / Chen, C.Y. / Lin, T.C. / Yeh, L.F. / Hsieh, W.C. / Gao, S. / Burnouf, P.A. / Chen, B.M. / Hsieh, T.J. / Dashnyam, P. / Kuo, Y.H. / Tu, Z. / Roffler, S.R. / Lin, C.H.

History

Deposition	Nov 20, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Aug 11, 2021	Group: Database references / Category: citation / citation_author / database_2 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 22, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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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Download

PDBx/mmCIF format	6ldd.cif.gz	966.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ldd.ent.gz	798.9 KB	Display	PDB format
PDBx/mmJSON format	6ldd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ldd_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6ldd_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6ldd_validation.xml.gz	102.8 KB	Display
Data in CIF	6ldd_validation.cif.gz	153.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ld/6ldd ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6ldd	HTTPS FTP

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Related structure data

Related structure data	6ld0C 6ld6C 6ldbC 6ldcC 6legC 6lejC 6lelC 6lemC 3k46S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ldb-d 6ld6-d 5z1b-d 6ld0-d 6u7i-d 5z19-2 3lpf-1 5c70-1 6lel-1 6jz2-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (12) #39 - Mar 2003 lac Repressor similarity (12)

Deposited unit

A: LacZ1 Beta-galactosidase

B: LacZ1 Beta-galactosidase

C: LacZ1 Beta-galactosidase

D: LacZ1 Beta-galactosidase

hetero molecules

299 kDa, 4 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)	92.557, 105.623, 161.987
Angle α, β, γ (deg.)	90.000, 91.300, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: -1 - 667 / Label seq-ID: 1 - 669

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B
3	chain C	C	C
4	chain D	D	D

#1: Protein	LacZ1 Beta-galactosidase Mass: 74588.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) (bacteria) Strain: ATCC 27534 / DSM 20436 / JCM 1195 / Bd1 / Gene: lacZ1, BDP_2112 / Production host: Escherichia coli (E. coli) / References: UniProt: D2Q7B1, beta-galactosidase
#2: Chemical	ChemComp-CKX / (2~{S},3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-2-propyl-piperidine-3-carboxylic acid Mass: 203.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₇NO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1949 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.64 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium cacodylate, pH 6.5, 8% w/v PEG 20K

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Data collection

Diffraction

Mean temperature: 110 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13C1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.2→30 Å / Num. obs: 155860 / % possible obs: 99.9 % / Redundancy: 4.6 % / B_iso Wilson estimate: 24.5 Å² / R_merge(I) obs: 0.08 / Χ²: 0.945 / Net I/σ(I): 9 / Num. measured all: 722951

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.2-2.28	4.6	0.42	15511	0.851	1	100
2.28-2.37	4.7	0.365	15551	0.816	1	100
2.37-2.48	4.7	0.279	15498	0.833	1	100
2.48-2.61	4.7	0.221	15533	0.864	1	100
2.61-2.77	4.7	0.165	15539	0.921	1	100
2.77-2.99	4.7	0.121	15583	0.996	1	100
2.99-3.29	4.7	0.083	15577	1.111	1	99.9
3.29-3.76	4.6	0.064	15573	1.194	1	99.9
3.76-4.73	4.5	0.05	15626	1.174	1	99.9
4.73-30	4.6	0.036	15869	0.7	1	99.9

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.25	data extraction
Blu-Ice		data collection
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3k46

3k46

Resolution: 2.205→29.583 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.95

	R_factor	Num. reflection	% reflection
R_free	0.1922	1926	1.39 %
R_work	0.1531	-	-
obs	0.1536	138710	88.3 %

Solvent computation

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

Displacement parameters

B_iso max: 138.5 Å² / B_iso mean: 23.91 Å² / B_iso min: 3.33 Å²

Refinement step

Cycle: final / Resolution: 2.205→29.583 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19636	0	56	1949	21641
B_iso mean	-	-	22.31	30.7	-
Num. residues	-	-	-	-	2480

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	20216
X-RAY DIFFRACTION	f_angle_d	0.995	27504
X-RAY DIFFRACTION	f_chiral_restr	0.04	2896
X-RAY DIFFRACTION	f_plane_restr	0.006	3644
X-RAY DIFFRACTION	f_dihedral_angle_d	13.281	7216

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	11687	X-RAY DIFFRACTION	6.116	TORSIONAL
1	2	B	11687	X-RAY DIFFRACTION	6.116	TORSIONAL
1	3	C	11687	X-RAY DIFFRACTION	6.116	TORSIONAL
1	4	D	11687	X-RAY DIFFRACTION	6.116	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.205-2.2596	0.2414	54	0.1762	4005	36
2.2596-2.3207	0.2383	93	0.1805	6125	56
2.3207-2.3889	0.2178	115	0.1757	8645	78
2.3889-2.466	0.2319	142	0.172	9786	89
2.466-2.5541	0.2209	151	0.1715	10260	93
2.5541-2.6563	0.2238	142	0.1702	10485	95
2.6563-2.7771	0.1923	151	0.1675	10589	96
2.7771-2.9234	0.2041	143	0.1641	10747	97
2.9234-3.1064	0.2024	161	0.1628	10829	98
3.1064-3.3459	0.2022	152	0.1525	10917	99
3.3459-3.6821	0.1926	155	0.1494	10973	99
3.6821-4.2136	0.1749	154	0.1332	11044	99
4.2136-5.3037	0.1529	159	0.1234	11104	100
5.3037-29.583	0.176	154	0.1614	11275	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	0.0215	0.0007	-0.0047	0.0005	-0.0002	0.0011	-0.0033	0.0158	0.0021	0.0127	-0.0076	-0.0004	-0.0041	0.0002	-0.0015	0.0855	0.0165	-0.0124	0.0289	0.0013	0.0978	-26.6647	32.3786	-77.2674
2	0.0039	0.0032	0.0016	0.0068	-0.0004	0.001	-0.0016	0.0003	0.0172	0.001	-0.0037	0.0056	0.0019	0.0028	-0	0.0738	0.0188	0.0246	0.0316	0.0132	0.0712	-33.1662	36.6626	-70.8058
3	0.0064	-0.0042	0.0032	0.0027	-0.0021	0.0017	-0.0047	-0.0107	0.0043	0.0071	0.0039	-0.0017	-0.0053	-0.0069	-0.0041	0.0704	0.0147	0.0037	0.0271	-0.0255	0.0598	-34.8504	39.1973	-53.9036
4	0.0108	0.004	0.0058	0.0047	0.0058	0.0067	-0.0121	0.0392	-0.018	-0.0331	-0.004	0.02	-0.0134	-0.0063	-0.0003	0.1475	-0.0191	-0.0406	0.0965	-0.012	0.1307	-46.9509	8.8851	-87.6957
5	0.0641	0.0098	0.019	0.039	-0.0153	0.0401	0.0071	-0.035	-0.0114	-0.0045	0.0116	0.0461	-0.0139	-0.0399	0.0161	0.03	-0.0007	-0.0048	0.0402	0.0015	0.0766	-46.2837	16.7361	-59.7283
6	0.0059	-0.0065	0.0043	0.0085	-0.0056	0.0038	0.0216	0.0083	-0.0183	-0.0133	-0.0076	-0.0142	0.0378	-0.0042	0.0162	0.1074	0.0094	-0.0075	0.0172	-0.0199	0.0965	-18.1696	4.6317	-79.7471
7	0.0135	0.0014	0.0046	0.0006	0.0008	0.0021	-0.0041	-0.0167	-0.0079	0.0047	0.005	-0.0083	0.0083	0.0034	0.0076	0.0998	0.0174	-0.0128	0.0319	0.0296	0.0991	-8.2762	-4.1904	-57.6188
8	0.0239	-0.0001	-0.0067	0.007	0.0109	0.0222	-0.0257	0.034	0.0111	-0.0228	-0.0198	-0.0295	-0.0154	0.0164	-0.0111	0.1465	-0.0258	0.0486	0.0645	0.0274	0.1222	2.6295	29.3728	-85.9022
9	0.0737	0.0108	-0.0071	0.0368	-0.0026	0.0148	0.0035	-0.0426	-0.017	-0.0275	0.005	-0.0606	0.0092	0.0167	0.0116	0.0328	-0.002	0.01	0.0217	0.0161	0.0805	1.3292	18.2027	-59.204
10	0.0135	0.0009	0.0002	0.0127	-0.0027	0.0011	-0.013	-0.0289	0.0023	0.0302	0.0161	0.003	-0.0092	0.0062	0.0023	0.1234	-0.0095	-0.0198	0.2535	0.0263	0.065	-8.5748	12.807	-4.7523
11	0.0047	0.0004	0.0016	0.0022	-0.0007	0.0008	-0.0015	-0.013	-0.0009	0.0022	-0.0062	-0.0099	-0.0019	-0.0005	0	0.1789	0.0021	-0.0335	0.2341	0.0246	0.133	-2.6287	7.7452	-11.2169
12	0.003	-0.0019	0.003	0.001	-0.0019	0.0028	0.0034	-0.0094	-0.0029	-0.0071	0.0014	-0.0127	0.0079	-0.0043	0	0.0995	0.0076	-0.0081	0.1544	0.0519	0.1063	1.2719	7.9811	-27.9649
13	0.0049	0.0018	-0.0052	0.0007	-0.0027	0.0058	0.0031	-0.0257	-0.0155	0.0195	0.0087	0.0135	0.0135	0.0069	0.0166	0.2291	-0.0395	0.0289	0.2726	0.1262	0.1547	-28.4676	-12.2476	2.4858
14	0.0001	-0.0035	0.0051	0.033	-0.0431	0.0513	0.0098	-0.1072	-0.0877	0.0288	-0.0082	0.001	0.088	0.0131	0.0156	0.0723	-0.0075	-0.0088	0.0784	0.1386	0.0429	-18.8916	-8.0283	-24.6412
15	0.0002	-0.0001	-0.0004	0.0111	0.0046	0.0025	-0.0058	-0.0324	0.0009	0.0498	0.0152	0.0163	0.005	0.001	0.0013	0.1445	-0.0006	0.0414	0.2883	0.0136	0.0879	-37.5097	15.7024	-3.8396
16	0.0014	0.0003	-0.0007	-0.0001	0.0004	0.0013	0.0019	0.0078	0.0014	-0.0189	0.0034	0.0125	0.0012	-0.0113	-0	0.0821	0.004	0.0108	0.1686	-0.0402	0.0954	-46.7518	25.2284	-25.9092
17	0.0002	0.0009	0.0006	0.0028	0.0032	0.0038	-0.0044	-0.0219	0.0103	0.013	0.0131	-0.0076	0.0029	-0.0089	0	0.2572	-0.0118	-0.008	0.2791	-0.0787	0.1809	-20.231	39.8555	3.6792
18	0.0073	0.0011	-0.0018	0.0006	-0.0001	0.0062	-0.0039	0.0031	0.005	0.0089	-0.004	0.005	-0.006	0.0015	0.0009	0.1964	-0.0187	-0.0304	0.2291	-0.0843	0.1144	-15.5018	40.9879	7.0135
19	0.0133	0.0036	-0.011	0.0257	-0.0059	0.0148	-0.014	-0.1118	0.0637	0.04	-0.03	0.0144	-0.0845	-0.0353	-0.0405	0.1358	0.0205	-0.0103	0.149	-0.0787	0.0956	-26.8273	38.9253	-22.0787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 117 )	A	-1 - 117
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 118 through 154 )	A	118 - 154
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 155 through 189 )	A	155 - 189
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 325 )	A	190 - 325
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 326 through 667 )	A	326 - 667
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -1 through 134 )	B	-1 - 134
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 135 through 189 )	B	135 - 189
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 190 through 325 )	B	190 - 325
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 326 through 667 )	B	326 - 667
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -1 through 117 )	C	-1 - 117
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 118 through 154 )	C	118 - 154
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 155 through 189 )	C	155 - 189
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 190 through 325 )	C	190 - 325
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 326 through 667 )	C	326 - 667
15	X-RAY DIFFRACTION	15	chain 'D' and (resid -1 through 134 )	D	-1 - 134
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 135 through 189 )	D	135 - 189
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 190 through 234 )	D	190 - 234
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 235 through 325 )	D	235 - 325
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 326 through 667 )	D	326 - 667

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