PDB-6pkg: Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylgluc...

ID or keywords:

Entry

Database: PDB / ID: 6pkg

Title

Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide

Components

N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase

Keywords

HYDROLASE /

uncovering enzyme /

mannose 6-phosphate / glycosidase /

pro-peptide

Function / homology

Function and homology information

secretion of lysosomal enzymes / anatomical structure development /

membrane
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Gorelik, A. / Illes, K. / Nagar, B.

Funding support

Canada, 1items

Citation

Journal: Structure / Year: 2020
Title: Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.
Authors: Gorelik, A. / Illes, K. / Nagar, B.

History

Deposition	Jun 29, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 11, 2020	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 15, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen 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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6pkg.cif.gz	363.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6pkg.ent.gz	308.9 KB	Display	PDB format
PDBx/mmJSON format	6pkg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pk/6pkg ftp://data.pdbj.org/pub/pdb/validation_reports/pk/6pkg	HTTPS FTP

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Related structure data

Related structure data	6pkhC 6pkiC 6pkuC 6pkyC 6u11C C: citing same article (ref.)
Similar structure data	4xag-d 4xaz-d 6for-1 1s0j-d 5efz-1 4i75-d 1ms1-2 6fu6-d 1ms3-1 2ah2-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	#134 - Feb 2011 Integrin similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #75 - Mar 2006 Tissue Factor similarity (1)

Deposited unit

A: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase

B: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase

hetero molecules

83.2 kDa, 2 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)	124.356, 124.356, 278.792
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase / Mass: 35633.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: nagpa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1QSF9

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Sugars , 2 types, 4 molecules

#2: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...

Type: oligosaccharide

/ Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 321 molecules

#4: Chemical	... ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: I
#5: Chemical	ChemComp-I2I / molecular iodine / Iodine Mass: 253.809 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I₂
#6: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 7.56 Å³/Da / Density % sol: 83.73 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 50% PEG 200, 0.1M HEPES pH 6.4, soaked in 1M NaI

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.7712 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7712 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. obs: 90810 / % possible obs: 98.9 % / Redundancy: 20 % / Net I/σ(I): 16.1
Reflection shell	Resolution: 2.8→2.9 Å / Num. unique obs: 4913

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Processing

Software

Name	Version	Classification
PHENIX	(1.15_3459: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→35.658 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1

	R_factor	Num. reflection	% reflection
R_free	0.2081	3478	3.83 %
R_work	0.1831	-	-
obs	0.184	90810	88.3 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→35.658 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4748	0	210	257	5215

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4998
X-RAY DIFFRACTION	f_angle_d	0.542	6755
X-RAY DIFFRACTION	f_dihedral_angle_d	11.159	2958
X-RAY DIFFRACTION	f_chiral_restr	0.044	766
X-RAY DIFFRACTION	f_plane_restr	0.002	881

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 (%)
2.8001-2.8384	0.3138	57	0.3257	1491	X-RAY DIFFRACTION	37
2.8384-2.8789	0.3118	66	0.2999	1591	X-RAY DIFFRACTION	41
2.8789-2.9219	0.3484	75	0.2748	1816	X-RAY DIFFRACTION	46
2.9219-2.9675	0.3085	87	0.2907	2143	X-RAY DIFFRACTION	54
2.9675-3.0161	0.3129	97	0.2858	2445	X-RAY DIFFRACTION	62
3.0161-3.0681	0.3157	127	0.2793	3109	X-RAY DIFFRACTION	79
3.0681-3.1239	0.2603	144	0.2894	3749	X-RAY DIFFRACTION	93
3.1239-3.1839	0.2879	157	0.2783	3859	X-RAY DIFFRACTION	98
3.1839-3.2489	0.2816	157	0.2584	3947	X-RAY DIFFRACTION	100
3.2489-3.3195	0.2759	157	0.2213	3939	X-RAY DIFFRACTION	100
3.3195-3.3966	0.2184	163	0.2052	3969	X-RAY DIFFRACTION	100
3.3966-3.4815	0.2005	150	0.1911	3937	X-RAY DIFFRACTION	100
3.4815-3.5756	0.1904	153	0.1752	3948	X-RAY DIFFRACTION	100
3.5756-3.6807	0.2096	161	0.1723	3963	X-RAY DIFFRACTION	100
3.6807-3.7993	0.2231	157	0.153	3941	X-RAY DIFFRACTION	100
3.7993-3.935	0.1811	156	0.1436	3946	X-RAY DIFFRACTION	100
3.935-4.0923	0.141	153	0.1243	3975	X-RAY DIFFRACTION	100
4.0923-4.2783	0.1281	158	0.1182	3962	X-RAY DIFFRACTION	100
4.2783-4.5034	0.1223	154	0.1174	3925	X-RAY DIFFRACTION	100
4.5034-4.7849	0.153	162	0.1153	3951	X-RAY DIFFRACTION	100
4.7849-5.1534	0.1568	155	0.1387	3947	X-RAY DIFFRACTION	100
5.1534-5.6701	0.185	154	0.1569	3959	X-RAY DIFFRACTION	100
5.6701-6.4863	0.2577	161	0.2001	3950	X-RAY DIFFRACTION	100
6.4863-8.1559	0.2511	159	0.2105	3932	X-RAY DIFFRACTION	100
8.1559-35.658	0.2531	158	0.2444	3938	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	3.7568	-2.6233	-4.0171	2.6483	0.8368	6.3002	0.0366	0.3103	0.2296	-0.244	0.0473	0.1282	0.1306	-0.795	-0.0374	0.5214	-0.156	-0.1227	0.5196	-0.0262	0.3688	69.1113	24.5957	68.8586
2	3.6454	1.3782	-0.2738	4.3012	-2.4652	3.261	-0.1857	-0.2524	-0.7456	0.1398	-0.1925	-0.3122	0.8795	0.9057	0.4298	0.6204	0.1556	0.0826	0.2916	0.0588	0.5438	90.5696	15.597	78.0935
3	3.4589	-0.396	0.0663	4.1646	3.3147	3.1688	0.0899	0.1612	0.6042	-0.1675	-0.2196	-0.7983	-0.4485	0.1774	0.2526	0.2982	-0.1153	0.0579	0.3369	-0.0096	0.4718	74.3395	29.7034	92.4183
4	2.5727	0.2273	-0.8615	1.5494	-0.4894	2.6052	-0.2017	0.2804	-0.5774	-0.4689	0.0236	0.119	0.8371	-0.3272	0.1763	0.6405	-0.1061	0.0125	0.2863	-0.0432	0.5256	72.222	10.0974	77.1729
5	2.6483	0.9752	-0.0543	4.5798	0.3389	3.311	0.0466	0.2958	-0.3861	-0.599	-0.0516	-0.4858	0.5575	0.0712	-0.0132	0.4215	0.0017	0.0863	0.2623	-0.014	0.3323	84.4821	18.4746	72.2364
6	3.9784	-1.3249	0.2474	4.367	-0.2455	2.3426	-0.0885	0.0761	0.1109	-0.102	0.0022	0.0152	0.0633	-0.1	0.05	0.2608	-0.1122	0.0333	0.2255	0.0186	0.2466	77.0163	26.7431	82.8424
7	3.2097	-1.0729	-1.2657	7.2601	1.6018	4.3705	0.003	-0.0234	-0.1393	-0.3964	0.0227	0.1826	0.7033	-0.832	-0.0326	0.4118	-0.227	-0.019	0.4113	0.0133	0.3324	61.9454	18.6361	85.3632
8	3.5705	-3.352	-4.1343	4.1746	2.9646	6.1729	-0.2119	-0.9168	0.3379	0.3887	0.456	-0.2356	0.1678	0.5748	-0.3606	0.4715	-0.0598	-0.0039	0.6171	-0.0407	0.45	58.9808	33.5422	117.0203
9	1.6563	-0.4629	-0.004	1.6977	-0.6122	1.6477	-0.0668	0.5173	-0.1101	-0.1396	0.1225	0.3663	0.0488	-1.1326	0.0144	0.3539	-0.2077	0.0421	0.8029	0.1345	0.5999	35.3019	31.1863	109.8639
10	4.8685	2.3225	-2.9057	2.5794	-3.5854	4.9748	0.1895	0.1141	0.2887	0.0724	0.0539	0.2812	-0.2592	-0.612	-0.1757	0.322	-0.0714	0.0285	0.4682	0.0762	0.4357	54.3168	33.746	92.7596
11	4.6476	0.7557	0.4236	4.429	0.8055	3.1292	0.2734	-0.3858	-0.7756	0.5763	-0.0748	-0.1078	0.7278	-0.1178	-0.2207	0.5093	-0.1587	0.0871	0.4447	0.1564	0.4607	51.964	15.4834	111.5102
12	2.472	-2.1562	-1.6581	3.8865	1.4553	5.1494	-0.1322	-0.2652	-0.3076	0.4623	0.1535	0.0217	0.5588	0.2154	0.0392	0.3629	-0.1558	-0.0104	0.4026	0.0849	0.4411	56.5319	19.7748	111.141
13	2.7487	0.8072	1.3922	3.083	0.2921	2.1349	-0.0591	-0.5892	-0.3243	0.1688	-0.0589	0.1753	0.3748	-0.5949	0.1619	0.3684	-0.1467	0.0728	0.6064	0.116	0.4016	40.4421	22.8283	116.4741
14	6.7166	-1.7624	0.2433	7.7023	-3.1056	6.1465	0.1044	-0.6621	0.8426	0.6526	0.221	0.1446	-0.7726	-0.6259	-0.3912	0.2805	-0.0599	0.1207	0.4367	0.0293	0.4102	45.154	40.3823	112.4393
15	5.8228	2.7685	-1.0658	4.6195	0.3527	3.2201	-0.1372	0.319	0.4017	-0.2129	0.2541	-0.073	-0.0315	-0.193	-0.119	0.2754	-0.0708	-0.0137	0.2845	0.0701	0.3338	53.2568	34.728	103.4023
16	5.6774	-1.0581	-1.7823	2.5066	0.4924	3.7817	0.0154	0.239	0.0467	-0.0769	0.0387	0.02	0.0585	-0.2335	-0.0783	0.2842	-0.1233	-0.0138	0.3018	0.0749	0.2381	55.7701	29.3626	101.2312
17	5.0898	-1.2383	-1.0918	2.2327	-0.4105	5.2807	0.1509	0.008	-0.4811	0.2938	-0.1418	-0.0691	0.4454	0.1618	-0.0255	0.3775	-0.0886	-0.0254	0.2557	0.0459	0.3065	59.0767	19.7238	104.7667

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 106 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 107 through 190 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 191 through 235 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 236 through 299 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 300 through 336 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 30 through 49 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 50 through 79 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 106 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 107 through 131 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 132 through 160 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 161 through 209 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 235 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 236 through 275 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 276 through 319 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 320 through 336 )

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Sugars , 2 types, 4 molecules

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Non-polymers , 4 types, 321 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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