PDB-4ur9: Structure of ligand bound glycosylhydrolase

ID or keywords:

Entry

Database: PDB / ID: 4ur9

Title

Structure of ligand bound glycosylhydrolase

Components

O-GLCNACASE BT_4395

Keywords

HYDROLASE

Function / homology

Function and homology information

protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding
Similarity search - Function

Biological species

BACTEROIDES THETAIOTAOMICRON (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.2 Å

Authors

Darby, J.F. / Landstroem, J. / Roth, C. / He, Y. / Schultz, M. / Davies, G.J. / Hubbard, R.E.

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Discovery of Selective Small-Molecule Activators of a Bacterial Glycoside Hydrolase.
Authors: Darby, J.F. / Landstrom, J. / Roth, C. / He, Y. / Davies, G.J. / Hubbard, R.E.

History

Deposition	Jun 27, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ur9.cif.gz	800.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ur9.ent.gz	683.8 KB	Display	PDB format
PDBx/mmJSON format	4ur9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ur9_validation.pdf.gz	1006.4 KB	Display	wwPDB validaton report
Full document	4ur9_full_validation.pdf.gz	1022.8 KB	Display
Data in XML	4ur9_validation.xml.gz	51.8 KB	Display
Data in CIF	4ur9_validation.cif.gz	71.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/4ur9 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4ur9	HTTPS FTP

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Related structure data

Similar structure data	5abg-1 2chn-2 5abh-1 2cho-2 5abe-1 5fl0-1 5mi7-d 2chn-1 2x0h-2 2xm1-1 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	#141 - Sep 2011 O-GlcNAc Transferase similarity (9)

Deposited unit

A: O-GLCNACASE BT_4395

B: O-GLCNACASE BT_4395

hetero molecules

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

1

A: O-GLCNACASE BT_4395

hetero molecules

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

2

B: O-GLCNACASE BT_4395

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.486, 162.735, 223.179
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	O-GLCNACASE BT_4395 / N-ACETYL BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / GH84 / ...N-ACETYL BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / GH84 / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDASE Mass: 82316.109 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Chemical	ChemComp-BK9 / 4-ethoxyquinazoline Mass: 174.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₀N₂O
#3: Chemical	ChemComp-OAN / O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE / PUGNAc Mass: 353.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₁₉N₃O₇ / Comment: inhibitor*YM
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.8 Å³/Da / Density % sol: 55.6 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97625
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 130125 / % possible obs: 99.5 % / Observed criterion σ(I): 0.84 / Redundancy: 6.7 % / R_merge(I) obs: 0.16 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 6.5 % / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 0.84 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→48.786 Å / SU ML: 0.36 / σ(F): 1.27 / Phase error: 31.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.252	9154	5 %
R_work	0.2215	-	-
obs	0.2231	96246	99.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2→48.786 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10977	0	77	405	11459

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11326
X-RAY DIFFRACTION	f_angle_d	0.774	15334
X-RAY DIFFRACTION	f_dihedral_angle_d	12.422	4248
X-RAY DIFFRACTION	f_chiral_restr	0.031	1632
X-RAY DIFFRACTION	f_plane_restr	0.004	1977

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 (%)
2.1999-2.2249	0.4384	256	0.3962	5810	X-RAY DIFFRACTION	98
2.2249-2.2511	0.4742	289	0.3913	5716	X-RAY DIFFRACTION	98
2.2511-2.2785	0.3743	303	0.3733	5738	X-RAY DIFFRACTION	99
2.2785-2.3074	0.3801	305	0.3495	5813	X-RAY DIFFRACTION	100
2.3074-2.3377	0.3817	285	0.3402	5876	X-RAY DIFFRACTION	99
2.3377-2.3698	0.3856	329	0.3308	5667	X-RAY DIFFRACTION	99
2.3698-2.4036	0.326	322	0.3261	5791	X-RAY DIFFRACTION	100
2.4036-2.4395	0.3398	337	0.3212	5864	X-RAY DIFFRACTION	100
2.4395-2.4776	0.3469	274	0.3121	5758	X-RAY DIFFRACTION	99
2.4776-2.5182	0.2976	298	0.2932	5777	X-RAY DIFFRACTION	100
2.5182-2.5617	0.2961	261	0.2844	5886	X-RAY DIFFRACTION	100
2.5617-2.6082	0.3666	266	0.2856	5806	X-RAY DIFFRACTION	99
2.6082-2.6584	0.2929	297	0.2684	5814	X-RAY DIFFRACTION	100
2.6584-2.7127	0.2685	246	0.269	5948	X-RAY DIFFRACTION	99
2.7127-2.7716	0.3179	293	0.2477	5681	X-RAY DIFFRACTION	100
2.7716-2.8361	0.2619	309	0.2362	5892	X-RAY DIFFRACTION	100
2.8361-2.907	0.2917	305	0.2419	5762	X-RAY DIFFRACTION	100
2.907-2.9856	0.2766	340	0.2304	5782	X-RAY DIFFRACTION	100
2.9856-3.0735	0.2483	326	0.2238	5803	X-RAY DIFFRACTION	100
3.0735-3.1726	0.2844	271	0.2283	5828	X-RAY DIFFRACTION	100
3.1726-3.286	0.2557	329	0.2249	5763	X-RAY DIFFRACTION	99
3.286-3.4175	0.2909	333	0.2094	5844	X-RAY DIFFRACTION	100
3.4175-3.573	0.2476	309	0.194	5743	X-RAY DIFFRACTION	100
3.573-3.7614	0.1959	315	0.1925	5807	X-RAY DIFFRACTION	100
3.7614-3.9969	0.2005	317	0.1828	5854	X-RAY DIFFRACTION	100
3.9969-4.3053	0.1994	351	0.1714	5770	X-RAY DIFFRACTION	100
4.3053-4.7383	0.1968	297	0.1571	5810	X-RAY DIFFRACTION	100
4.7383-5.4232	0.1967	351	0.1642	5733	X-RAY DIFFRACTION	100
5.4232-6.8296	0.2491	342	0.1964	5818	X-RAY DIFFRACTION	100
6.8296-48.7982	0.1885	298	0.1817	5785	X-RAY DIFFRACTION	99

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	1.4802	-0.4268	0.4374	2.016	0.3509	2.4935	-0.2885	0.718	-0.445	-0.792	0.5164	0.154	0.5949	-0.5676	-0.1853	0.6294	-0.3991	-0.0343	1.1025	-0.0706	0.3736	17.2326	25.9154	220.0331
2	1.4987	0.3914	-0.4366	0.7171	-0.3871	2.2747	-0.0115	0.1029	0.0601	0.0053	0.1244	0.0305	-0.1228	-0.2757	-0.0968	0.139	0.0217	-0.0124	0.6012	0.0836	0.185	24.855	45.4538	243.0157
3	1.0842	-0.4778	-0.6131	1.5871	1.2693	4.0186	0.0125	-0.1203	0.0393	0.2626	-0.0313	0.1241	0.1308	-0.6523	0.1087	0.2049	0.003	-0.0347	0.6028	0.1787	0.213	8.9206	34.6883	271.1189
4	4.776	0.194	-1.2357	0.3926	-0.1677	0.6846	0.1211	-0.2583	0.5241	0.2276	0.0359	0.0165	-0.3665	-0.5766	-0.1959	0.3609	0.1236	0.0123	0.6399	0.036	0.2546	11.9118	47.287	274.2696
5	5.4582	0.3273	-0.4586	3.3131	-1.4532	0.677	-0.0153	-0.7368	0.3929	0.2494	-0.1806	0.1261	-1.1684	-0.4819	0.1983	1.0083	0.2653	-0.2277	0.5206	-0.0892	0.384	26.2576	57.0213	282.249
6	9.5917	-2.1437	-2.124	8.838	-2.3163	6.0293	-0.0716	-0.2583	0.9011	0.3802	0.1776	-0.6311	-1.4113	0.8488	-0.0927	0.7648	-0.0768	-0.2831	0.372	-0.0024	0.4943	31.6918	57.3311	280.5444
7	2.5299	-0.6181	-0.5633	5.9103	2.3764	0.9887	-0.0704	-0.4284	-0.0054	0.1218	-0.0716	0.1158	-0.1494	-0.0141	0.2011	0.3088	-0.0713	0.0067	0.6296	0.0088	0.0263	12.9443	30.1616	316.4106
8	2.7972	0.5809	0.6977	5.2351	2.1957	5.7433	-0.0221	-0.352	0.2366	0.0952	-0.0088	0.0924	-0.3932	0.0623	0.0378	0.1487	-0.0108	0.0177	0.5226	-0.0645	0.1619	18.1423	28.0236	318.7027
9	4.061	-0.5063	0.0618	2.3037	-0.2079	1.8888	-0.0546	-0.1822	-0.2572	0.0531	-0.0334	-0.285	0.2357	0.3176	0.0823	0.1939	-0.0043	-0.0084	0.41	0.0059	0.2154	38.8846	9.4311	300.408
10	4.328	0.2144	1.0426	3.5987	-2.8423	6.7473	-0.1124	-0.0669	-0.7692	-0.1458	-0.1	-0.2737	0.7325	-0.2848	0.1585	0.2733	-0.0248	0.0814	0.2789	-0.0399	0.32	25.2851	-3.8841	299.9903
11	1.2362	-0.1764	0.0929	0.5135	-0.2434	1.3381	-0.0665	0.305	-0.0759	-0.1122	0.1951	0.1994	0.2105	-0.6363	-0.1014	0.2114	-0.1591	-0.0222	0.5343	0.015	0.1941	8.6728	14.4872	288.5169
12	1.137	0.0772	1.2257	1.6109	0.6128	1.4636	-0.1622	0.4389	0.1214	-0.408	0.118	0.1325	0.1768	-0.8065	-0.0257	0.3139	-0.2465	-0.0011	0.8095	0.1091	0.226	8.6282	19.5947	267.6352
13	3.6878	-2.082	3.2702	1.5067	-1.4784	3.577	0.3932	0.6963	-0.4167	-0.3204	-0.0173	0.1545	0.6771	-0.1325	-0.4282	0.439	-0.2101	-0.0197	0.6594	-0.0562	0.2293	8.3507	9.458	269.1566
14	6.8406	-1.9634	0.7737	3.128	0.1772	1.9603	0.1889	0.6516	0.1366	-0.5172	-0.1206	-0.1644	0.8643	-0.0865	-0.086	0.9236	-0.1504	0.0229	0.8037	-0.0509	0.2686	20.0471	3.9585	255.8872
15	7.3232	-1.2552	3.5838	2.9116	0.2389	6.8512	0.1359	0.3465	0.3733	-0.7484	0.0776	-0.847	1.0905	0.7245	-0.2221	0.98	0.0814	0.1881	0.8247	0.0793	0.5456	30.5641	-0.6488	252.6643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 5 THROUGH 128 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 129 THROUGH 488 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 489 THROUGH 544 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 545 THROUGH 616 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 617 THROUGH 667 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 668 THROUGH 716 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 3 THROUGH 34 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 35 THROUGH 128 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 129 THROUGH 278 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 279 THROUGH 348 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 349 THROUGH 488 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 489 THROUGH 544 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 545 THROUGH 579 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 580 THROUGH 662 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 663 THROUGH 716 )

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