PDB-6kal: Crystal structure of FKRP in complex with Mg ion and CMP

ID or keywords:

Entry

Database: PDB / ID: 6kal

Title

Crystal structure of FKRP in complex with Mg ion and CMP

Components

Fukutin-related protein

Keywords

TRANSFERASE / glycosyltranferase / phospho ribitoyl tranferase

Function / homology

Function and homology information

Matriglycan biosynthesis on DAG1 / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phosphotransferase activity, for other substituted phosphate groups / protein O-linked glycosylation via mannose / catalytic complex / rough endoplasmic reticulum / protein tetramerization / sarcolemma / Golgi membrane / Golgi apparatus ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Kuwabara, N.

Funding support

Japan, 2items

Citation

Journal: Nat Commun / Year: 2020
Title: Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.
Authors: Kuwabara, N. / Imae, R. / Manya, H. / Tanaka, T. / Mizuno, M. / Tsumoto, H. / Kanagawa, M. / Kobayashi, K. / Toda, T. / Senda, T. / Endo, T. / Kato, R.

History

Deposition	Jun 23, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn_type.id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6kal.cif.gz	703.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6kal.ent.gz	587.6 KB	Display	PDB format
PDBx/mmJSON format	6kal.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	6kajC 6kakC 6kamC 6kanC 6l7sC 6l7tC 6l7uC C: citing same article (ref.)
Similar structure data	6l7t-d 6l7u-d 6kan-d 6l7s-d 6kak-d 6kam-d 6kaj-d 2fsf-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

Deposited unit

A: Fukutin-related protein

B: Fukutin-related protein

C: Fukutin-related protein

D: Fukutin-related protein

hetero molecules

203 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	77.583, 118.674, 252.695
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Sugars , 2 types, 11 molecules ABCD

#1: Protein

Fukutin-related protein / Ribitol-5-phosphate transferase

Mass: 50026.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: FKRP / Cell line (production host): HEK293S GnT- / Production host:

Homo sapiens (human) / References: UniProt: Q9H9S5

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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, 275 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₄N₃O₈P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 4-8% PEG 4,000, 0.1 M HEPES-NaOH (pH7.5) and 0.2 M MgCl2

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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: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→48.9962 Å / Num. obs: 72606 / % possible obs: 99.93 % / Redundancy: 6.7 % / Net I/σ(I): 13.56
Reflection shell	Resolution: 2.6→2.6342 Å / Num. unique obs: 2628

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→48.987 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04

	R_factor	Num. reflection	% reflection
R_free	0.2409	3680	5.07 %
R_work	0.1947	-	-
obs	0.1971	72606	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→48.987 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13701	0	194	259	14154

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	14317
X-RAY DIFFRACTION	f_angle_d	1.002	19635
X-RAY DIFFRACTION	f_dihedral_angle_d	7.408	9991
X-RAY DIFFRACTION	f_chiral_restr	0.056	2187
X-RAY DIFFRACTION	f_plane_restr	0.009	2582

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 (%)
2.6-2.6342	0.3816	136	0.33	2628	X-RAY DIFFRACTION	100
2.6342-2.6703	0.3366	142	0.3263	2601	X-RAY DIFFRACTION	100
2.6703-2.7084	0.3463	133	0.2984	2601	X-RAY DIFFRACTION	100
2.7084-2.7489	0.3388	149	0.276	2619	X-RAY DIFFRACTION	100
2.7489-2.7918	0.3202	136	0.2628	2618	X-RAY DIFFRACTION	100
2.7918-2.8376	0.3287	148	0.2603	2624	X-RAY DIFFRACTION	100
2.8376-2.8865	0.3427	127	0.259	2617	X-RAY DIFFRACTION	100
2.8865-2.939	0.3233	148	0.2576	2619	X-RAY DIFFRACTION	100
2.939-2.9955	0.2772	136	0.256	2627	X-RAY DIFFRACTION	100
2.9955-3.0566	0.3411	138	0.2529	2622	X-RAY DIFFRACTION	100
3.0566-3.1231	0.2898	129	0.2355	2653	X-RAY DIFFRACTION	100
3.1231-3.1957	0.285	145	0.2325	2610	X-RAY DIFFRACTION	100
3.1957-3.2756	0.264	147	0.2223	2607	X-RAY DIFFRACTION	100
3.2756-3.3642	0.2812	155	0.2116	2660	X-RAY DIFFRACTION	100
3.3642-3.4632	0.2545	133	0.2103	2614	X-RAY DIFFRACTION	100
3.4632-3.5749	0.2588	130	0.2073	2663	X-RAY DIFFRACTION	100
3.5749-3.7026	0.2197	142	0.1976	2651	X-RAY DIFFRACTION	100
3.7026-3.8508	0.2349	158	0.1808	2643	X-RAY DIFFRACTION	100
3.8508-4.026	0.2087	123	0.1702	2653	X-RAY DIFFRACTION	100
4.026-4.2382	0.2388	157	0.1621	2648	X-RAY DIFFRACTION	100
4.2382-4.5035	0.1927	142	0.1511	2657	X-RAY DIFFRACTION	100
4.5035-4.8509	0.1779	136	0.1446	2704	X-RAY DIFFRACTION	100
4.8509-5.3386	0.1856	161	0.1604	2654	X-RAY DIFFRACTION	100
5.3386-6.1098	0.2324	140	0.1789	2716	X-RAY DIFFRACTION	100
6.1098-7.6929	0.1961	150	0.1737	2742	X-RAY DIFFRACTION	100
7.6929-48.9962	0.1903	139	0.1614	2875	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	1.8681	0.9801	0.3943	2.0184	0.0266	2.3611	-0.0455	-0.0866	0.3167	-0.0562	-0.0557	0.4037	-0.3925	-0.5542	0.1065	0.5653	0.1376	-0.0091	0.4527	-0.0101	0.4435	-8.0727	241.9153	34.6439
2	3.6186	0.6177	2.4164	0.8388	1.2125	2.2112	0.0719	-0.2214	-0.1207	0.3163	-0.0228	-0.1615	0.0883	-0.1422	-0.0356	0.5418	0.0451	0.01	0.3604	0.0411	0.3585	15.3817	236.8902	51.0235
3	5.2262	-1.0881	2.8773	4.5144	1.0001	6.6635	-0.0705	-0.0117	0.2768	0.6234	0.186	-1.1295	0.3057	1.0131	-0.068	0.5845	0.0274	-0.1092	0.526	0.0245	0.5895	35.7104	241.5841	64.916
4	1.6702	-0.3815	-0.847	1.1895	-0.9225	5.5325	-0.1868	0.1729	0.7658	-0.0716	0.0218	-0.7871	-0.5241	0.309	0.1253	0.8244	-0.0953	-0.1279	0.5326	0.0342	0.993	28.8282	255.9445	61.3593
5	1.9806	0.8958	0.4423	2.9972	0.3677	1.8564	0.0449	0.2687	-0.1723	-0.3725	0.1373	-0.5535	-0.144	0.3014	-0.1441	0.5748	0.005	0.0997	0.3941	-0.0304	0.4909	24.3801	242.5296	17.4334
6	1.7405	0.4435	0.0739	6.0368	0.013	2.9258	0.044	-0.2079	-0.1958	0.2512	-0.0423	-0.0244	0.2127	-0.2303	0.0136	0.353	0.015	-0.0478	0.3439	0.0385	0.3633	2.0476	202.9794	16.1555
7	1.6371	0.4563	-0.5118	2.0673	-0.0658	1.9765	-0.0753	-0.1955	-0.1322	0.0552	-0.1217	-0.41	0.2537	0.4418	0.1824	0.4806	0.0609	-0.0322	0.4154	0.0778	0.4127	44.1238	277.3632	37.3283
8	2.2982	-0.7418	-1.7058	3.9157	-0.0918	3.9893	0.0213	-0.1029	-0.0831	0.3757	-0.0625	0.6363	-0.1381	-0.3706	0.037	0.5403	-0.0316	0.033	0.4319	-0.0648	0.4187	7.0161	273.5325	63.03
9	2.7013	0.4637	-0.211	4.0585	-0.3172	2.3803	-0.1278	0.1273	-0.1999	-0.312	0.2099	0.377	0.4692	-0.2505	-0.0774	0.6366	-0.0364	-0.0464	0.3634	0.0268	0.3893	7.8611	268.8918	23.5944
10	0.7798	-0.0888	0.0011	1.5836	-0.3954	1.263	-0.0419	0.0163	-0.0858	0.0199	-0.0049	-0.0327	0.0684	-0.0028	0.0307	0.5338	-0.0528	-0.0142	0.312	-0.0498	0.4064	16.3943	267.9924	33.164
11	1.5201	-0.4477	-0.5106	2.6665	-0.7833	1.6662	-0.1298	0.6385	-0.2486	-0.4159	0.031	0.2015	0.3912	-0.1149	0.0018	0.7173	-0.0261	-0.0497	0.382	-0.0244	0.3457	14.4091	268.7582	19.3493
12	2.3492	1.1922	-0.1794	2.9886	-0.678	1.3103	-0.1384	0.3022	0.1267	-0.5637	0.1884	0.4086	0.0127	-0.1435	-0.0543	0.6583	0.004	-0.1054	0.4145	0.0512	0.4136	13.2345	282.488	15.2491
13	2.7115	0.7885	-0.7288	3.3423	-0.7846	2.174	0.2626	-0.2492	-0.0483	0.0559	-0.1983	0.0318	-0.051	0.1706	-0.0104	0.4877	0.0042	-0.0365	0.3181	0.0222	0.322	28.6603	300.5557	21.6083
14	2.6379	1.0718	-0.6071	3.5908	-0.8308	3.0581	0.3669	-0.5701	0.4132	0.8047	-0.2698	-0.1413	-0.8094	0.5539	-0.1279	0.6788	-0.159	0.0017	0.4691	-0.0404	0.4115	33.922	320.5309	24.3312
15	2.8962	1.4755	-0.3955	3.8049	-0.495	3.2486	0.0669	-0.2052	0.2267	0.3858	-0.1751	-0.8457	-0.7744	0.9084	0.0357	0.8271	-0.2107	0.0404	0.5795	-0.0438	0.6926	43.0902	324.7413	15.0621
16	1.7277	-0.7683	0.5301	4.8761	-2.4773	3.0679	0.146	0.1035	0.0172	-0.511	-0.4668	-0.7346	0.115	0.7294	0.3568	0.4889	-0.0103	0.0852	0.4517	0.0646	0.4504	40.4845	315.1857	8.9295

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 46 through 250 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 251 through 336 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 337 through 454 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 455 through 492 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 47 through 272 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 273 through 491 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 47 through 289 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 290 through 492 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 47 through 83 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 84 through 111 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 112 through 139 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 140 through 272 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 273 through 315 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 316 through 428 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 429 through 454 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 455 through 491 )

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