PDB-7xtm: Crystal structure of the C-terminal domain of Bombyx mori N-acety...

ID or keywords:

Entry

Database: PDB / ID: 7xtm

Title

Crystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV

Components

N-acetylglucosaminyltransferase IV

Keywords

SUGAR BINDING PROTEIN / glycosyltransferase / N-glycan / N-glycosylation / Golgi / N-acetylglucosamine / carbohydrate-binding module / lectin

Biological species

Bombyx mori (domestic silkworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.47 Å

Authors

Miyazaki, T. / Oka, N. / Mori, S.

Funding support

Japan, 1items

Citation

Journal: Glycobiology / Year: 2022
Title: Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family.
Authors: Oka, N. / Mori, S. / Ikegaya, M. / Park, E.Y. / Miyazaki, T.

History

Deposition	May 17, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2022	Group: Database references / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2	Dec 7, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7xtm.cif.gz	124.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7xtm.ent.gz	94.2 KB	Display	PDB format
PDBx/mmJSON format	7xtm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7xtm_validation.pdf.gz	454.7 KB	Display	wwPDB validaton report
Full document	7xtm_full_validation.pdf.gz	455.6 KB	Display
Data in XML	7xtm_validation.xml.gz	13.9 KB	Display
Data in CIF	7xtm_validation.cif.gz	19.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtm ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtm	HTTPS FTP

-
Related structure data

Related structure data	7xtlC 7xtnC C: citing same article (ref.)

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: N-acetylglucosaminyltransferase IV

B: N-acetylglucosaminyltransferase IV

hetero molecules

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

1

A: N-acetylglucosaminyltransferase IV

hetero molecules

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

2

B: N-acetylglucosaminyltransferase IV

hetero molecules

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

Unit cell

Length a, b, c (Å)	32.733, 64.466, 78.810
Angle α, β, γ (deg.)	90.000, 95.092, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	N-acetylglucosaminyltransferase IV Mass: 19040.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GB:BDI24347.2 / Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: MGAT4 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MES-NaOH, pH 7.0, 12%(w/v) PEG20000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.47→39.25 Å / Num. obs: 53654 / % possible obs: 96.6 % / Redundancy: 6.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.052 / R_pim(I) all: 0.022 / R_rim(I) all: 0.057 / Net I/σ(I): 18.2
Reflection shell	Resolution: 1.47→1.55 Å / Redundancy: 5 % / R_merge(I) obs: 0.526 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6660 / CC_1/2: 0.841 / R_pim(I) all: 0.255 / R_rim(I) all: 0.588 / % possible all: 83

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 1.47→33.547 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.933 / SU B: 3.375 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2484	2686	5.013 %
R_work	0.2244	50895	-
all	0.226	-	-
obs	-	53581	96.454 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 21.258 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.6 Å²	0 Å²	0.134 Å²
2-	-	-1.848 Å²	-0 Å²
3-	-	-	2.386 Å²

Refinement step

Cycle: LAST / Resolution: 1.47→33.547 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2317	0	24	152	2493

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2457
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2203
X-RAY DIFFRACTION	r_angle_refined_deg	1.729	1.651	3344
X-RAY DIFFRACTION	r_angle_other_deg	1.457	1.58	5085
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.001	5	289
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.856	23.624	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.794	15	387
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.439	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	311
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	2812
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	616
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	396
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	2106
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	1137
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1176
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	135
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.116	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.141	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.117	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	0.82	1.042	1126
X-RAY DIFFRACTION	r_mcbond_other	0.814	1.04	1125
X-RAY DIFFRACTION	r_mcangle_it	1.337	1.558	1407
X-RAY DIFFRACTION	r_mcangle_other	1.337	1.56	1408
X-RAY DIFFRACTION	r_scbond_it	1.151	1.242	1331
X-RAY DIFFRACTION	r_scbond_other	1.151	1.244	1332
X-RAY DIFFRACTION	r_scangle_it	1.803	1.796	1931
X-RAY DIFFRACTION	r_scangle_other	1.802	1.798	1932
X-RAY DIFFRACTION	r_lrange_it	4.226	12.647	2680
X-RAY DIFFRACTION	r_lrange_other	4.203	12.44	2660

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 (%)
1.47-1.508	0.359	145	0.3	2963	X-RAY DIFFRACTION	75.7864
1.508-1.549	0.277	158	0.28	3394	X-RAY DIFFRACTION	89.4035
1.549-1.594	0.273	201	0.271	3423	X-RAY DIFFRACTION	94.081
1.594-1.643	0.279	215	0.258	3495	X-RAY DIFFRACTION	96.8163
1.643-1.697	0.261	194	0.242	3373	X-RAY DIFFRACTION	98.5904
1.697-1.757	0.293	171	0.246	3344	X-RAY DIFFRACTION	99.3218
1.757-1.823	0.267	165	0.257	3230	X-RAY DIFFRACTION	99.211
1.823-1.898	0.287	172	0.248	3050	X-RAY DIFFRACTION	99.047
1.898-1.982	0.225	152	0.229	2986	X-RAY DIFFRACTION	99.5558
1.982-2.079	0.249	161	0.229	2856	X-RAY DIFFRACTION	99.5381
2.079-2.191	0.251	124	0.224	2765	X-RAY DIFFRACTION	99.7583
2.191-2.324	0.259	131	0.216	2561	X-RAY DIFFRACTION	99.7406
2.324-2.484	0.265	131	0.227	2416	X-RAY DIFFRACTION	99.7259
2.484-2.683	0.242	145	0.221	2220	X-RAY DIFFRACTION	99.6629
2.683-2.938	0.247	110	0.218	2083	X-RAY DIFFRACTION	99.8179
2.938-3.285	0.248	93	0.22	1913	X-RAY DIFFRACTION	100
3.285-3.792	0.214	66	0.211	1670	X-RAY DIFFRACTION	99.9424
3.792-4.641	0.195	74	0.183	1423	X-RAY DIFFRACTION	99.8
4.641-6.552	0.268	52	0.221	1112	X-RAY DIFFRACTION	99.5723
6.552-33.547	0.277	26	0.253	618	X-RAY DIFFRACTION	99.5363

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	1.6414	1.0281	0.3366	5.929	1.0295	2.134	-0.0295	-0.0175	0.0876	-0.0728	-0.0586	0.3582	-0.0642	-0.1483	0.0881	0.054	0.0046	0.006	0.1472	-0.0014	0.09	5.1003	1.3202	4.7377
2	0.8737	0.1999	0.3612	2.1063	0.1288	0.3911	0.0327	-0.1188	-0.0574	0.3235	-0.0484	0.1721	0.0865	-0.091	0.0157	0.1393	-0.0086	0.0275	0.1714	-0.0003	0.0264	11.1505	-0.4969	15.593
3	0.5104	0.2535	0.259	2.3253	0.9075	1.1604	0.0156	0.0071	0.0099	-0.0506	-0.0805	0.1606	0.0143	-0.0915	0.0649	0.0977	0.0011	-0.0049	0.1449	-0.0052	0.0389	12.0297	-1.6127	1.9207
4	0.0664	0.2873	0.1266	2.1177	0.8024	1.3404	0.0381	-0.0065	-0.0353	-0.0558	0.0294	-0.1825	0.0084	0.0533	-0.0675	0.1008	0.0005	-0.0114	0.1418	-0.0065	0.0269	20.7617	-2.8272	4.3263
5	0.5216	-0.0346	0.2756	1.3848	0.545	0.3772	0.0279	0.0792	0.0212	-0.0685	-0.0039	-0.0891	-0.0096	0.0589	-0.024	0.1352	-0.0072	0.0054	0.1538	0.0004	0.0108	19.3219	-0.0071	-1.4145
6	1.149	0.0544	0.3831	1.6189	-0.0281	0.7864	0.0313	-0.0184	-0.0727	0.2237	-0.0091	0.0065	-0.0278	0.0228	-0.0222	0.1173	-0.0022	-0.0104	0.1551	0.0054	0.0059	19.3795	3.6006	13.7109
7	1.2468	-1.9593	2.6394	5.9858	1.0271	18.4779	0.0842	0.1095	-0.0486	-0.4002	-0.1734	0.5661	0.1802	-0.274	0.0892	0.1676	-0.0601	-0.1078	0.1682	0.067	0.224	7.4267	0.4226	-5.8308
8	1.6138	0.4764	0.3975	7.5928	0.9378	1.7608	0.0023	0.0459	-0.0359	0.0064	0.0271	0.2315	0.0527	-0.0896	-0.0295	0.0611	-0.0122	-0.0189	0.1756	0.0023	0.0757	17.7804	-32.4003	34.9558
9	0.4837	-0.5962	0.3578	1.3712	-0.2236	0.5464	0.0736	0.0598	0.0603	-0.23	-0.1289	0.0625	-0.0027	-0.0249	0.0553	0.1495	0.0031	-0.0287	0.1896	0.0091	0.0439	23.9897	-29.985	24.2607
10	0.5859	-0.5487	0.0958	3.379	0.8547	1.5196	0.0128	-0.002	0.0065	0.1247	-0.063	0.0486	0.0068	-0.1045	0.0502	0.1116	-0.0126	-0.0194	0.1634	0.0074	0.0071	24.497	-29.6037	38.1023
11	0.0695	-0.1475	0.2331	2.0438	0.3286	1.2458	0.0136	0.037	0.0311	0.0981	-0.0617	-0.2162	0.037	0.0689	0.0482	0.1083	-0.0046	-0.0212	0.159	0.0101	0.0309	33.9668	-28.4791	35.0722
12	1.9329	0.3775	-0.3921	1.6989	0.681	0.4341	0.1263	-0.0858	-0.0879	0.2168	-0.0704	-0.201	0.0519	-0.005	-0.0559	0.209	0.0021	-0.0758	0.1597	0.0218	0.0394	31.8995	-31.3835	41.7556
13	0.757	-0.8709	-0.2902	1.7796	0.0469	0.5129	0.0473	0.0396	0.1303	-0.0385	-0.013	-0.0351	0.1065	-0.0623	-0.0342	0.1335	-0.0117	0.0117	0.1742	0.0011	0.0563	28.1626	-32.6307	32.433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	409 - 421
2	X-RAY DIFFRACTION	2	ALL	A	422 - 454
3	X-RAY DIFFRACTION	3	ALL	A	455 - 476
4	X-RAY DIFFRACTION	4	ALL	A	477 - 502
5	X-RAY DIFFRACTION	5	ALL	A	503 - 526
6	X-RAY DIFFRACTION	6	ALL	A	527 - 541
7	X-RAY DIFFRACTION	7	ALL	A	542 - 547
8	X-RAY DIFFRACTION	8	ALL	B	409 - 421
9	X-RAY DIFFRACTION	9	ALL	B	422 - 456
10	X-RAY DIFFRACTION	10	ALL	B	457 - 476
11	X-RAY DIFFRACTION	11	ALL	B	477 - 503
12	X-RAY DIFFRACTION	12	ALL	B	504 - 524
13	X-RAY DIFFRACTION	13	ALL	B	525 - 548

-
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://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