PDB-5fl1: Structure of a hydrolase with an inhibitor

ID or keywords:

Entry

Database: PDB / ID: 5fl1

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 2.0	Aug 29, 2018	Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author 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 / _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 2.1	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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 "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5fl1.cif.gz	808 KB	Display	PDBx/mmCIF format
PDB format	pdb5fl1.ent.gz	690.4 KB	Display	PDB format
PDBx/mmJSON format	5fl1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5fl1_validation.pdf.gz	928.6 KB	Display	wwPDB validaton report
Full document	5fl1_full_validation.pdf.gz	953.2 KB	Display
Data in XML	5fl1_validation.xml.gz	52.4 KB	Display
Data in CIF	5fl1_validation.cif.gz	75.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fl/5fl1 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/5fl1	HTTPS FTP

-
Related structure data

Related structure data	5fkyC 5fl0C C: citing same article (ref.)
Similar structure data	5cxb-d 6lhb-d 1696 5mi7-d 4izh-d 5ogl-d 3mfb-d 6aku-d 5abh-1 5abg-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

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

Unit cell

Length a, b, c (Å)	51.499, 162.113, 223.213
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-DV1 / (3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-5-(hydroxymethyl)-2-(prop-2-enylamino)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]thiazole-6,7-diol / Propyleneaminothiazoline Mass: 260.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₂O₄S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#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.: 570 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 55.3 % / Description: NONE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.95→49.08 Å / Num. obs: 137650 / % possible obs: 99.8 % / Observed criterion σ(I): 0.9 / Redundancy: 13.2 % / B_iso Wilson estimate: 27.26 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 12 % / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

-
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→49.082 Å / SU ML: 0.2 / σ(F): 0.02 / Phase error: 29.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2216	12250	5 %
R_work	0.1934	-	-
obs	0.1948	137650	92.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 48.33 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→49.082 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11110	0	51	570	11731

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11452
X-RAY DIFFRACTION	f_angle_d	0.897	15511
X-RAY DIFFRACTION	f_dihedral_angle_d	15.049	4318
X-RAY DIFFRACTION	f_chiral_restr	0.046	1653
X-RAY DIFFRACTION	f_plane_restr	0.006	2003

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 (%)
1.9479-1.9701	0.3467	322	0.2935	5990	X-RAY DIFFRACTION	72
1.9701-1.9932	0.3158	384	0.2708	6379	X-RAY DIFFRACTION	77
1.9932-2.0175	0.3267	322	0.2693	6504	X-RAY DIFFRACTION	78
2.0175-2.0431	0.2907	366	0.2614	6638	X-RAY DIFFRACTION	79
2.0431-2.07	0.3269	364	0.2695	6812	X-RAY DIFFRACTION	81
2.07-2.0983	0.2717	363	0.258	6792	X-RAY DIFFRACTION	82
2.0983-2.1283	0.2704	321	0.2376	7148	X-RAY DIFFRACTION	84
2.1283-2.1601	0.2595	380	0.2282	7208	X-RAY DIFFRACTION	86
2.1601-2.1938	0.2333	362	0.2288	7254	X-RAY DIFFRACTION	87
2.1938-2.2298	0.2712	336	0.2298	7484	X-RAY DIFFRACTION	88
2.2298-2.2682	0.3103	395	0.2699	7449	X-RAY DIFFRACTION	90
2.2682-2.3095	0.2652	401	0.2052	7691	X-RAY DIFFRACTION	92
2.3095-2.3539	0.2386	419	0.2076	8000	X-RAY DIFFRACTION	95
2.3539-2.4019	0.269	462	0.2165	7965	X-RAY DIFFRACTION	96
2.4019-2.4542	0.2481	437	0.2147	8296	X-RAY DIFFRACTION	98
2.4542-2.5113	0.2641	425	0.2019	8215	X-RAY DIFFRACTION	100
2.5113-2.5741	0.2341	385	0.1941	8515	X-RAY DIFFRACTION	100
2.5741-2.6437	0.2551	386	0.2037	8298	X-RAY DIFFRACTION	100
2.6437-2.7214	0.2013	414	0.2044	8424	X-RAY DIFFRACTION	100
2.7214-2.8093	0.2553	370	0.1965	8366	X-RAY DIFFRACTION	100
2.8093-2.9097	0.2426	476	0.1924	8357	X-RAY DIFFRACTION	100
2.9097-3.0261	0.2515	482	0.1962	8341	X-RAY DIFFRACTION	100
3.0261-3.1639	0.2162	416	0.2013	8363	X-RAY DIFFRACTION	100
3.1639-3.3306	0.2355	452	0.1992	8312	X-RAY DIFFRACTION	100
3.3306-3.5392	0.2277	478	0.1878	8343	X-RAY DIFFRACTION	100
3.5392-3.8124	0.1883	467	0.1765	8312	X-RAY DIFFRACTION	100
3.8124-4.1959	0.1845	477	0.1607	8332	X-RAY DIFFRACTION	100
4.1959-4.8026	0.1611	439	0.1442	8354	X-RAY DIFFRACTION	100
4.8026-6.049	0.1792	489	0.1628	8313	X-RAY DIFFRACTION	100
6.049-49.0975	0.2034	460	0.1877	8334	X-RAY DIFFRACTION	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	1.0836	0.0914	-0.3046	1.2342	-1.0151	1.0396	-0.3349	1.0877	-0.3177	-0.7079	0.4494	0.1496	0.5708	-0.7471	0.0481	0.5978	-0.3952	-0.0277	1.0893	-0.1258	0.3551	19.6461	28.983	224.8654
2	2.1042	0.4098	-0.7794	0.8274	-0.4384	1.849	0.0218	0.4835	0.215	-0.0248	0.1502	0.0688	-0.1043	-0.2997	-0.1392	0.2411	0.0039	0.0033	0.4487	0.1131	0.2335	28.8593	47.8275	240.1561
3	7.4055	-5.927	-3.0076	5.9327	2.9807	2.8948	0.0162	0.1135	-0.1889	-0.1306	-0.1396	0.253	-0.1403	-0.4735	0.1458	0.306	-0.0697	-0.0218	0.6123	0.0572	0.2545	-0.7021	37.5186	261.4174
4	3.0385	-0.4269	-1.561	0.195	0.5553	2.5665	0.0233	-0.2232	-0.1813	0.1041	-0.0543	0.1098	0.1945	-0.4449	0.095	0.2812	-0.0258	-0.0072	0.4421	0.126	0.2581	11.1626	36.4666	269.3686
5	3.1629	0.0648	0.2211	0.4179	-0.2085	1.1955	-0.1998	-0.3992	0.8195	0.195	0.0558	-0.0435	-0.6833	-0.5188	0.0915	0.5648	0.1324	-0.0574	0.6174	-0.0528	0.4776	15.8624	53.3755	279.4101
6	5.9971	-3.3544	0.2489	6.4242	-2.0323	1.7411	-0.146	-0.2895	0.9023	0.2596	0.1136	-0.279	-1.3868	0.2963	-0.037	0.9465	0.036	-0.2006	0.4856	-0.023	0.5915	29.2453	60.2076	282.072
7	1.7935	-0.1936	-0.7076	1.6071	1.3016	3.1257	0.0128	-0.4914	0.3177	0.1182	-0.0053	0.007	-0.2917	-0.0146	0.0035	0.2567	-0.0202	-0.0135	0.3585	-0.0804	0.2721	18.9744	26.4218	314.2734
8	2.1231	0.0769	-0.108	0.856	-0.312	1.1682	-0.0868	-0.0527	-0.3624	-0.045	0.0624	-0.0863	0.1539	-0.0304	0.0065	0.2259	-0.0542	0.0348	0.171	-0.0223	0.2395	28.3829	6.2944	298.8691
9	1.9044	-0.4033	0.4485	0.8812	-0.0139	1.8092	-0.0289	0.3538	-0.1712	-0.1782	0.0421	0.2083	0.1618	-0.4658	-0.0323	0.3777	-0.1642	-0.0084	0.5567	0.0395	0.3205	5.2035	15.7695	270.0796
10	3.9153	-2.3695	-2.6724	4.8193	-0.4178	3.1714	0.3342	0.2187	0.0595	-0.2611	-0.2646	-0.2302	0.4075	0.2444	0.097	0.8716	-0.0041	-0.0231	0.809	-0.0441	0.5357	26.3715	0.5441	253.6639

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 163 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 164 THROUGH 440 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 441 THROUGH 488 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 489 THROUGH 560 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 561 THROUGH 662 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 663 THROUGH 715 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 3 THROUGH 155 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 156 THROUGH 440 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 441 THROUGH 593 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 594 THROUGH 715 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi