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

ID or keywords:

Entry

Database: PDB / ID: 6ldc

Title

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

Components

LacZ1 Beta-galactosidase

Keywords

HYDROLASE / inhibitor / glycosidase / isofagomine

Function / homology

Function and homology information

: / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function

Biological species

Bifidobacterium dentium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.181 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	6ldc.cif.gz	956 KB	Display	PDBx/mmCIF format
PDB format	pdb6ldc.ent.gz	789.9 KB	Display	PDB format
PDBx/mmJSON format	6ldc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ldc_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6ldc_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6ldc_validation.xml.gz	104.5 KB	Display
Data in CIF	6ldc_validation.cif.gz	155 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ld/6ldc ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6ldc	HTTPS FTP

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Related structure data

Related structure data	6ld0C 6ld6C 6ldbC 6lddC 6legC 6lejC 6lelC 6lemC 3k46S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hq6-d 5z1b-d 6ld0-d 6hq8-d 6lu1-d 6lej-1 4kt0-d 6leg-d 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

300 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)	92.659, 105.144, 160.967
Angle α, β, γ (deg.)	90.000, 91.090, 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-E9O / (2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid Mass: 287.395 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2030 / 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: 2.63 Å³/Da / Density % sol: 53.19 %
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: 2.18→30 Å / Num. obs: 160237 / % possible obs: 99.9 % / Redundancy: 4.6 % / B_iso Wilson estimate: 22.05 Å² / R_merge(I) obs: 0.05 / Χ²: 1.01 / Net I/σ(I): 15.2 / Num. measured all: 738778

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.18-2.26	4.6	0.168	15991	1.097	1	99.9
2.26-2.35	4.6	0.142	15859	1.073	1	100
2.35-2.46	4.7	0.118	16021	1.045	1	100
2.46-2.58	4.7	0.095	15986	1.009	1	100
2.58-2.75	4.7	0.074	15990	0.961	1	100
2.75-2.96	4.7	0.057	15953	0.926	1	100
2.96-3.26	4.7	0.041	16029	0.875	1	100
3.26-3.73	4.7	0.036	16050	0.945	1	100
3.73-4.69	4.4	0.04	16067	1.469	1	99.9
4.69-30	4.5	0.027	16291	0.727	1	99.8

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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: 2.181→28.056 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.57

	R_factor	Num. reflection	% reflection
R_free	0.1766	1990	1.26 %
R_work	0.1499	-	-
obs	0.1503	158521	98.63 %

Solvent computation

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

Displacement parameters

B_iso max: 187.04 Å² / B_iso mean: 21.25 Å² / B_iso min: 3.94 Å²

Refinement step

Cycle: final / Resolution: 2.181→28.056 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19552	0	80	2030	21662
B_iso mean	-	-	21.23	29.52	-
Num. residues	-	-	-	-	2468

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	20152
X-RAY DIFFRACTION	f_angle_d	1.107	27400
X-RAY DIFFRACTION	f_chiral_restr	0.048	2884
X-RAY DIFFRACTION	f_plane_restr	0.007	3620
X-RAY DIFFRACTION	f_dihedral_angle_d	13.471	7208

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	11607	X-RAY DIFFRACTION	6.8	TORSIONAL
1	2	B	11607	X-RAY DIFFRACTION	6.8	TORSIONAL
1	3	C	11607	X-RAY DIFFRACTION	6.8	TORSIONAL
1	4	D	11607	X-RAY DIFFRACTION	6.8	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 (%)
2.181-2.2353	0.2191	132	0.1663	10628	94
2.2353-2.2957	0.1986	138	0.1595	10927	97
2.2957-2.3632	0.1855	148	0.1563	11055	98
2.3632-2.4395	0.1963	144	0.1494	11080	98
2.4395-2.5266	0.1922	135	0.1551	11086	98
2.5266-2.6277	0.1905	144	0.1538	11173	99
2.6277-2.7472	0.1876	145	0.1532	11220	99
2.7472-2.8919	0.204	144	0.1589	11170	99
2.8919-3.0728	0.1922	144	0.1552	11269	100
3.0728-3.3098	0.1713	143	0.1476	11331	100
3.3098-3.6422	0.1767	143	0.1453	11304	100
3.6422-4.1678	0.1377	142	0.1341	11365	100
4.1678-5.2453	0.1493	144	0.1332	11378	100
5.2453-28.056	0.1879	144	0.1691	11545	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	0.0158	-0.0008	-0.0018	0.0021	-0.0012	0.0026	0.0216	0.0213	-0.0091	-0.0065	-0.0105	-0.0015	0.0245	-0.004	0.0021	0.0898	0.0117	-0.0011	0.0271	-0.011	0.0709	-18.1895	-18.3237	-78.5584
2	0.0012	-0.0008	-0.0011	0.0055	0.0026	0.0013	-0.0017	0.0035	-0.0136	-0.0152	-0.0042	-0.0035	-0.0012	-0.0036	-0.0001	0.1051	0.0122	-0.0238	0.0643	-0.0204	0.0914	-11.8582	-23.3982	-72.6135
3	0.0012	-0.0005	-0.0007	0.0004	0.0004	0.0011	-0.0076	-0.0057	-0.001	-0.0007	-0.0004	0.0034	0.0029	0.0067	-0	0.0941	0.0147	-0.0164	0.0532	0.0132	0.0903	-10.8571	-27.6763	-57.2542
4	0.007	0.0018	-0.0059	0.007	0.0025	0.0129	-0.0051	0.0369	0.0231	-0.0212	-0.0129	-0.0211	-0.0066	0.0008	-0.0026	0.1314	-0.0168	0.0464	0.0805	0.0414	0.1114	2.3783	6.1586	-85.6993
5	0.0282	0.0099	0.0055	0.0267	0.0047	0.0164	0.0037	-0.021	0.0006	-0.0219	0.0006	-0.0631	0.0035	-0.0024	-0	0.0536	0.0029	0.0014	0.0521	0.0082	0.103	1.1165	-4.9982	-59.0215
6	0.0149	0.0014	-0.0017	0.0077	-0.0018	0.0017	-0.0022	-0.0266	0.0064	0.0264	0.0081	0.0014	-0.003	0.0068	0.0026	0.1034	-0.0162	-0.0223	0.2036	0.0135	0.0467	-8.3727	-10.2492	-3.6823
7	0.0022	-0.0015	0.0021	0.0007	-0.0012	0.0017	0.0031	-0.0088	0.0004	-0.0109	-0.0055	-0.0105	0.0063	-0.002	-0	0.1011	0.0137	-0.0039	0.1476	0.0352	0.0969	0.8562	-17.3552	-25.6676
8	0.003	0.0019	-0.0037	0.0005	-0.0027	0.0045	0.0025	-0.0216	-0.0153	0.0185	0.0099	0.0132	0.0087	0.004	0.0084	0.1894	-0.0455	0.0349	0.2183	0.1154	0.1145	-28.3812	-35.5839	2.5431
9	0.0121	0.0057	0.004	0.0222	-0.0141	0.0303	-0.0073	-0.0969	-0.0743	0.0272	-0.0236	0.003	0.0767	0.0072	-0.0394	0.0797	0.0022	0.0042	0.0547	0.1323	0.0395	-18.9186	-31.3459	-24.4913
10	0.0175	-0	-0.0053	0.0027	-0.0026	0.0039	-0.0025	0.0271	0.0102	-0.0024	-0.009	-0.0095	-0.0039	-0.0051	-0.0029	0.0694	0.0127	-0.0123	0.0319	0.0152	0.0878	-26.9109	9.1995	-76.9292
11	0.0009	-0.0002	0.001	0.0037	-0.0011	0.0008	-0.0063	0.0004	0.0179	-0.0013	-0.0078	0.0048	-0.0012	0.0013	0	0.0776	0.0193	0.0106	0.0522	0.0219	0.0901	-33.3402	13.4606	-70.4688
12	0.0017	-0.0006	0.0002	0.0007	0.0001	0.0004	-0.011	-0.007	0.0026	-0.0035	0.0006	-0.0049	-0.0013	-0.0071	0.0001	0.0667	0.0129	-0.0044	0.0517	-0.011	0.0893	-34.5777	15.837	-54.8646
13	0.0053	0.0019	0.0053	0.0004	0.0012	0.0043	-0.0061	0.0357	-0.0123	-0.0188	-0.0029	0.0168	-0.0003	-0.0063	-0.0002	0.0917	-0.0316	-0.0513	0.0688	-0.0314	0.0784	-47.2511	-14.2603	-87.3718
14	0.028	0.0103	-0.0038	0.0207	-0.0068	0.0144	-0.0016	-0.0099	-0.0079	-0.0161	0.0115	0.0541	-0.0021	-0.018	0	0.0433	0.0027	-0.0043	0.0632	-0.0002	0.0947	-46.4611	-6.4603	-59.4581
15	0.01	-0.0005	-0.0004	0.0082	0.0015	0.0022	-0.0093	-0.0238	-0.0074	0.0373	0.0125	0.0099	0.0002	-0.0085	0.0019	0.1409	-0.0029	0.0387	0.2288	0.002	0.0568	-37.5364	-7.6817	-3.6668
16	0.0021	-0.001	-0.0016	0.0003	0.0008	0.001	-0.0014	-0.0071	0.0018	-0.0045	-0.0023	0.0099	-0.0034	-0.004	-0	0.111	0.0215	0.0123	0.1769	-0.0252	0.1031	-46.6115	1.6508	-24.8076
17	0.0002	0.0011	0.0005	0.0018	0.0019	0.0033	-0.0088	-0.0138	0.0131	0.0106	0.0086	-0.0091	0.005	-0.0033	0	0.2151	-0.0079	-0.0056	0.2165	-0.0686	0.1516	-20.3194	16.5209	3.9127
18	0.0018	0.0009	0.0019	0.0016	0.0015	0.002	-0.0006	0.0019	0.005	0.0085	0.0015	0.0015	-0.0033	0.0031	0	0.2005	-0.0119	-0.0295	0.2064	-0.0732	0.1346	-15.5614	17.5863	7.1835
19	0.0022	0.0022	0.0008	0.0252	0.0196	0.0217	-0.0171	-0.0857	0.0655	0.0632	-0.0188	0.0183	-0.073	-0.0524	-0.0425	0.0983	0.0527	-0.0022	0.0784	-0.1301	0.0247	-26.9597	15.6513	-21.8294

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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