PDB-5fl0: Structure of a hydrolase with an inhibitor

ID or keywords:

Entry

Database: PDB / ID: 5fl0

Title

Structure of a hydrolase with an inhibitor

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: 1.95 Å

Authors

Cekic, N. / Heinonen, J.E. / Stubbs, K.A. / Roth, C. / McEachern, E.J. / Davies, G.J. / Vocadlo, D.J.

Citation

Journal: Chem Sci / Year: 2016
Title: Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by humanO-GlcNAcase.
Authors: Cekic, N. / Heinonen, J.E. / Stubbs, K.A. / Roth, C. / He, Y. / Bennet, A.J. / McEachern, E.J. / Davies, G.J. / Vocadlo, D.J.

History

Deposition	Oct 20, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 31, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0	May 8, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site 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 / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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	5fl0.cif.gz	799.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5fl0.ent.gz	682.6 KB	Display	PDB format
PDBx/mmJSON format	5fl0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fl0_validation.pdf.gz	970.7 KB	Display	wwPDB validaton report
Full document	5fl0_full_validation.pdf.gz	990.8 KB	Display
Data in XML	5fl0_validation.xml.gz	50.9 KB	Display
Data in CIF	5fl0_validation.cif.gz	73.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fl/5fl0 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/5fl0	HTTPS FTP

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Related structure data

Related structure data	5fkyC 5fl1C C: citing same article (ref.)
Similar structure data	5abg-1 5abf-2 5mi4-d 5abe-1 5abg-2 5abf-1 2x0h-2 4ur9-1 5abh-1 2chn-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 (8)

Deposited unit

A: O-GLCNACASE BT_4395

B: O-GLCNACASE BT_4395

hetero molecules

165 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
82.7 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
82.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.529, 162.129, 223.643
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 / BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDASE / GLYCOSIDE HYDROLASE Mass: 82316.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-71I / (3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-(butylamino)-5-(hydroxymethyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d] [1,3]thiazole-6,7-diol / Butylaminothiazoline Mass: 276.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₂₀N₂O₄S
#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.: 557 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.7 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.95→44.96 Å / Num. obs: 137683 / % possible obs: 99.9 % / Observed criterion σ(I): 0.9 / Redundancy: 6.7 % / B_iso Wilson estimate: 31.77 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.95→44.963 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 28.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2273	13144	5 %
R_work	0.1996	-	-
obs	0.2011	137506	99.62 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→44.963 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10953	0	53	557	11563

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11318
X-RAY DIFFRACTION	f_angle_d	0.835	15333
X-RAY DIFFRACTION	f_dihedral_angle_d	13.928	4280
X-RAY DIFFRACTION	f_chiral_restr	0.043	1636
X-RAY DIFFRACTION	f_plane_restr	0.006	1987

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 (%)
1.95-1.9722	0.4277	444	0.4238	8370	X-RAY DIFFRACTION	100
1.9722-1.9954	0.401	472	0.4011	8337	X-RAY DIFFRACTION	100
1.9954-2.0197	0.4303	423	0.3762	8306	X-RAY DIFFRACTION	100
2.0197-2.0453	0.3809	467	0.3475	8297	X-RAY DIFFRACTION	100
2.0453-2.0722	0.3616	469	0.3196	8315	X-RAY DIFFRACTION	100
2.0722-2.1006	0.3315	443	0.3167	8242	X-RAY DIFFRACTION	100
2.1006-2.1306	0.3002	379	0.2971	8431	X-RAY DIFFRACTION	100
2.1306-2.1624	0.3284	430	0.278	8335	X-RAY DIFFRACTION	100
2.1624-2.1962	0.2579	418	0.2613	8278	X-RAY DIFFRACTION	100
2.1962-2.2322	0.2864	397	0.2481	8451	X-RAY DIFFRACTION	100
2.2322-2.2707	0.2787	422	0.2472	8248	X-RAY DIFFRACTION	99
2.2707-2.3119	0.2808	429	0.2347	8347	X-RAY DIFFRACTION	99
2.3119-2.3564	0.263	443	0.2205	8368	X-RAY DIFFRACTION	100
2.3564-2.4045	0.2707	475	0.2161	8244	X-RAY DIFFRACTION	100
2.4045-2.4568	0.2565	439	0.2192	8459	X-RAY DIFFRACTION	100
2.4568-2.5139	0.2228	424	0.2091	8228	X-RAY DIFFRACTION	100
2.5139-2.5768	0.2351	393	0.1966	8473	X-RAY DIFFRACTION	100
2.5768-2.6465	0.2565	381	0.1993	8273	X-RAY DIFFRACTION	100
2.6465-2.7243	0.2117	413	0.1896	8404	X-RAY DIFFRACTION	100
2.7243-2.8122	0.2237	370	0.1918	8346	X-RAY DIFFRACTION	100
2.8122-2.9127	0.2432	477	0.1966	8305	X-RAY DIFFRACTION	100
2.9127-3.0293	0.2626	481	0.1979	8369	X-RAY DIFFRACTION	100
3.0293-3.1672	0.1992	406	0.1888	8279	X-RAY DIFFRACTION	100
3.1672-3.3341	0.2419	452	0.1959	8309	X-RAY DIFFRACTION	100
3.3341-3.5429	0.2117	476	0.1832	8287	X-RAY DIFFRACTION	99
3.5429-3.8163	0.1924	461	0.1667	8299	X-RAY DIFFRACTION	100
3.8163-4.2001	0.1824	476	0.1652	8262	X-RAY DIFFRACTION	99
4.2001-4.8073	0.1696	437	0.1425	8331	X-RAY DIFFRACTION	100
4.8073-6.0544	0.19	489	0.159	8275	X-RAY DIFFRACTION	100
6.0544-44.9753	0.1875	458	0.1746	8282	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	1.0364	-0.3261	0.0293	1.1893	-0.053	1.1422	-0.2594	0.5062	-0.5208	-0.7778	0.4739	0.2266	0.789	-0.4669	-0.1866	0.9366	-0.446	-0.0179	1.1308	-0.1246	0.5488	17.9975	21.8746	219.6914
2	1.7863	0.2476	-0.288	1.9136	-0.5821	2.3254	-0.3168	0.9334	-0.2167	-0.5858	0.4083	0.09	0.4303	-0.6908	0.0825	0.4094	-0.2756	-0.0362	0.9757	-0.0187	0.2527	20.8471	32.7343	228.9617
3	2.0505	-0.1038	-0.5598	1.5052	-0.5054	1.8725	0.0077	0.2818	0.1902	-0.0206	0.0483	-0.0979	-0.1854	0.0293	-0.0594	0.2419	-0.0248	-0.0037	0.5447	0.07	0.25	38.8461	50.2711	238.1192
4	1.5653	0.3827	-0.3571	0.8544	-0.3759	1.7155	-0.0247	0.3671	0.1519	-0.0202	0.1863	0.185	0.0045	-0.5874	-0.1572	0.2648	0.006	0.0026	0.6723	0.1202	0.2878	16.345	44.718	243.4695
5	3.8795	-2.3015	-0.9383	2.7043	1.4452	1.5511	0.0365	0.0305	-0.1413	-0.0683	-0.218	0.3405	-0.1326	-0.5095	0.1809	0.4045	-0.0323	-0.0043	0.8202	0.0655	0.3325	-0.8307	37.8266	261.6021
6	2.2068	-0.2685	-0.7136	0.6946	0.7768	2.1801	0.0193	-0.2162	-0.1134	0.1069	-0.0858	0.0633	0.0825	-0.3375	0.0843	0.338	-0.0488	-0.0175	0.6214	0.1172	0.2818	8.821	34.6715	271.5461
7	1.9125	0.141	0.2009	0.4085	0.0694	0.117	-0.0677	-0.4193	0.433	0.1711	0.0048	-0.0084	-0.1718	-0.2906	0.0909	0.3684	0.0564	-0.0162	0.6613	0.0071	0.3121	11.8591	46.8772	274.6029
8	4.6514	-0.5343	1.2536	1.9931	-1.0054	5.8873	-0.5931	-0.4507	0.5111	0.005	0.0567	-0.3008	-1.7198	0.2116	0.5461	0.8583	0.055	-0.2062	0.6282	-0.0382	0.536	29.7607	54.8315	283.435
9	1.9107	0.4506	0.6353	3.016	1.6347	3.4307	-0.0913	-0.4113	0.3067	0.0443	-0.0012	0.1064	-0.3903	0.0052	0.0812	0.2998	-0.0188	0.0162	0.5864	-0.0901	0.2631	16.8411	28.6176	318.7363
10	2.0149	0.0666	0.0137	1.3109	-0.2493	1.0982	-0.045	-0.0956	-0.1578	-0.0197	-0.0265	-0.2615	0.1335	0.2089	0.0645	0.2981	-0.0557	0.0315	0.4601	-0.0205	0.3281	38.1039	8.4445	300.6351
11	4.0853	-0.3921	1.4839	1.3638	-0.9807	3.1234	-0.2179	-0.1139	-0.8049	-0.1595	0.0357	-0.0875	0.3962	-0.0863	-0.0539	0.4088	-0.1085	0.077	0.3497	0.0206	0.5352	27.6134	-6.5584	303.0458
12	1.6189	-0.1195	0.1873	1.1984	-0.5527	1.5758	-0.0418	0.0194	-0.1742	-0.0874	0.1038	0.0628	0.1691	-0.2914	-0.057	0.275	-0.1142	0.0167	0.4084	-0.0284	0.2504	15.9165	9.3401	296.2437
13	3.8699	0.786	0.7111	1.7944	0.8988	1.511	-0.0367	0.0786	-0.1024	0.0678	-0.1145	0.4198	0.1212	-0.6483	-0.0855	0.3677	-0.1586	-0.0101	0.7878	0.0562	0.3222	-0.8717	17.8292	278.3348
14	1.5474	-0.1096	1.1178	0.6853	0.0147	1.5957	0.0536	0.4014	-0.0457	-0.227	-0.0084	0.1544	0.1827	-0.3119	-0.0544	0.4261	-0.1597	0.0096	0.6934	0.0096	0.2942	8.2178	15.9324	268.6634
15	2.2185	-1.9183	0.1844	2.0309	-0.206	1.6239	0.0687	-0.03	-0.37	-0.3955	-0.1055	0.1184	0.5944	0.102	0.0658	0.8543	-0.0822	0.0177	0.8444	-0.0886	0.4396	17.9354	2.9949	256.5416
16	1.9642	-0.4397	0.6465	4.152	-0.0558	2.3998	0.1992	0.5165	-0.0876	-0.519	-0.1369	-0.8094	0.605	0.6863	-0.0697	1.0418	0.1329	0.1042	1.0674	-0.0455	0.6244	30.2635	-2.6701	252.5139

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 70 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 71 THROUGH 163 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 164 THROUGH 319 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 320 THROUGH 440 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 441 THROUGH 488 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 489 THROUGH 544 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 545 THROUGH 616 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 617 THROUGH 715 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 3 THROUGH 128 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 129 THROUGH 286 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 287 THROUGH 319 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 320 THROUGH 440 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 441 THROUGH 488 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 489 THROUGH 579 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 580 THROUGH 647 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 657 THROUGH 715 )

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