PDB-8b0d: Crystal structure of beta-glucuronidase from Acidobacterium capsu...

ID or keywords:

Entry

Database: PDB / ID: 8b0d

Title

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB151

Components

beta-glucuronidase from Acidobacterium capsulatum

Keywords

HYDROLASE / b-glucuronidase

Function / homology

Function and homology information

hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function

Biological species

Acidobacterium capsulatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.62 Å

Authors

Armstrong, Z. / Davies, G.J.

Funding support

United Kingdom, 1items

Citation

Journal: Chemmedchem / Year: 2023
Title: 4-O-Substituted Glucuronic Cyclophellitols are Selective Mechanism-Based Heparanase Inhibitors.
Authors: Borlandelli, V. / Armstrong, Z. / Nin-Hill, A. / Codee, J.D.C. / Raich, L. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.S.

History

Deposition	Sep 7, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2023	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Mar 1, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8b0d.cif.gz	180.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8b0d.ent.gz		Display	PDB format
PDBx/mmJSON format	8b0d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8b0d_validation.pdf.gz	748.3 KB	Display	wwPDB validaton report
Full document	8b0d_full_validation.pdf.gz	749.8 KB	Display
Data in XML	8b0d_validation.xml.gz	19.4 KB	Display
Data in CIF	8b0d_validation.cif.gz	29 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/8b0d ftp://data.pdbj.org/pub/pdb/validation_reports/b0/8b0d	HTTPS FTP

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Related structure data

Related structure data	8b0bC 8b0cC 8b0eC 5g0mS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

Deposited unit

AAA: beta-glucuronidase from Acidobacterium capsulatum

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	82.461, 43.605, 136.202
Angle α, β, γ (deg.)	90.000, 98.685, 90.000
Int Tables number	5
Space group name H-M	I121

#1: Protein	beta-glucuronidase from Acidobacterium capsulatum Mass: 50814.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidobacterium capsulatum (bacteria) Strain: ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161 Gene: ACP_2665 / Production host: Escherichia coli (E. coli) / References: UniProt: C1F2K5
#2: Chemical	ChemComp-ALA / ALANINE Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₂
#3: Chemical	ChemComp-OUU / (1~{S},2~{R},3~{R},4~{S},6~{S})-2-(2-acetamidoethoxy)-3,4,6-tris(oxidanyl)cyclohexane-1-carboxylic acid Mass: 277.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.38 Å³/Da / Density % sol: 48.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.62→74.924 Å / Num. obs: 61021 / % possible obs: 99.7 % / Redundancy: 6 % / CC_1/2: 0.99 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.62→1.65 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2988 / CC_1/2: 0.516

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5g0m

5g0m

Resolution: 1.62→74.924 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.956 / WR_factor R_free: 0.228 / WR_factor R_work: 0.199 / SU B: 3.307 / SU ML: 0.104 / Average fsc free: 0.7981 / Average fsc work: 0.8124 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2259	2969	4.866 %
R_work	0.1976	58052	-
all	0.199	-	-
obs	-	61021	99.577 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 36.771 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.693 Å²	-0 Å²	3.922 Å²
2-	-	0.278 Å²	-0 Å²
3-	-	-	-0.748 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→74.924 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3292	0	29	238	3559

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	3415
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3063
X-RAY DIFFRACTION	r_angle_refined_deg	1.567	1.648	4648
X-RAY DIFFRACTION	r_angle_other_deg	1.432	1.573	7092
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.554	5	432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.093	21.943	175
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.833	15	495
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.6	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	435
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3915
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	756
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	687
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	2800
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	1675
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1426
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	213
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.042	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.189	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.225	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.975	3.783	1737
X-RAY DIFFRACTION	r_mcbond_other	2.971	3.782	1736
X-RAY DIFFRACTION	r_mcangle_it	3.934	5.659	2166
X-RAY DIFFRACTION	r_mcangle_other	3.935	5.66	2167
X-RAY DIFFRACTION	r_scbond_it	3.403	4.066	1678
X-RAY DIFFRACTION	r_scbond_other	3.405	4.059	1675
X-RAY DIFFRACTION	r_scangle_it	4.945	5.984	2482
X-RAY DIFFRACTION	r_scangle_other	4.949	5.973	2477
X-RAY DIFFRACTION	r_lrange_it	6.463	44.442	3872
X-RAY DIFFRACTION	r_lrange_other	6.451	44.203	3826

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.62-1.662	0.367	235	0.356	4179	0.357	4463	0.5	0.495	98.9021	0.361
1.662-1.708	0.331	215	0.323	4123	0.323	4375	0.528	0.528	99.1543	0.323
1.708-1.757	0.324	200	0.307	4080	0.308	4315	0.601	0.615	99.1889	0.303
1.757-1.811	0.314	195	0.268	3884	0.271	4110	0.726	0.723	99.2457	0.263
1.811-1.87	0.275	181	0.252	3810	0.253	4016	0.762	0.779	99.3775	0.242
1.87-1.936	0.272	183	0.245	3693	0.246	3897	0.771	0.812	99.4611	0.235
1.936-2.009	0.269	180	0.22	3545	0.222	3737	0.823	0.85	99.6789	0.209
2.009-2.091	0.268	211	0.213	3433	0.216	3656	0.869	0.889	99.6718	0.204
2.091-2.184	0.235	163	0.191	3308	0.193	3481	0.911	0.922	99.7127	0.183
2.184-2.291	0.242	140	0.194	3170	0.196	3317	0.906	0.921	99.789	0.186
2.291-2.414	0.263	158	0.186	2999	0.19	3166	0.897	0.931	99.7157	0.181
2.414-2.561	0.238	129	0.182	2858	0.184	2990	0.925	0.94	99.8997	0.176
2.561-2.737	0.238	153	0.186	2671	0.189	2828	0.923	0.936	99.8586	0.183
2.737-2.956	0.26	130	0.203	2478	0.206	2608	0.902	0.925	100	0.202
2.956-3.238	0.232	111	0.201	2323	0.202	2434	0.929	0.935	100	0.202
3.238-3.619	0.193	106	0.178	2096	0.178	2202	0.942	0.954	100	0.184
3.619-4.177	0.148	75	0.156	1880	0.156	1955	0.964	0.963	100	0.165
4.177-5.112	0.178	91	0.153	1571	0.155	1663	0.969	0.969	99.9399	0.166
5.112-7.213	0.198	74	0.199	1234	0.199	1309	0.955	0.929	99.9236	0.205
7.213-74.924	0.192	39	0.208	718	0.207	759	0.954	0.957	99.7365	0.231

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