PDB-7eku: Crystal Structure of the Candida Glabrata Glycogen Debranching En...

ID or keywords:

Entry

Database: PDB / ID: 7eku

Title

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W958A)

Components

4-alpha-glucanotransferase

Keywords

SUGAR BINDING PROTEIN / Glycogen Debranching Enzyme

Function / homology

Function and homology information

amylo-alpha-1,6-glucosidase / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / cytoplasm
Similarity search - Function

Biological species

[Candida] glabrata CBS 138 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Shen, M. / Xiang, S.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W958A)
Authors: Shen, M. / Xiang, S.

History

Deposition	Apr 6, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7eku.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb7eku.ent.gz	1008.9 KB	Display	PDB format
PDBx/mmJSON format	7eku.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/ek/7eku ftp://data.pdbj.org/pub/pdb/validation_reports/ek/7eku	HTTPS FTP

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Related structure data

Related structure data	5d06S S: Starting model for refinement
Similar structure data	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	#74 - Feb 2006 alpha-Amylase similarity (2)

Deposited unit

A: 4-alpha-glucanotransferase

B: 4-alpha-glucanotransferase

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	160.221, 200.651, 259.976
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 3 through 283 or resid 288...
2	1	(chain B and resid 3 through 1527)

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	VAL	VAL	(chain A and (resid 3 through 283 or resid 288...	A	A	3 - 283	3 - 283
1	2	VAL	VAL	GLY	GLY	(chain A and (resid 3 through 283 or resid 288...	A	A	288 - 304	288 - 304
1	3	ALA	ALA	GLU	GLU	(chain A and (resid 3 through 283 or resid 288...	A	A	3 - 1527	3 - 1527
1	4	ASN	ASN	LYS	LYS	(chain A and (resid 3 through 283 or resid 288...	A	A	337 - 341	337 - 341
1	5	SER	SER	HIS	HIS	(chain A and (resid 3 through 283 or resid 288...	A	A	344 - 384	344 - 384
1	6	TYR	TYR	ASP	ASP	(chain A and (resid 3 through 283 or resid 288...	A	A	388 - 432	388 - 432
1	7	ILE	ILE	GLU	GLU	(chain A and (resid 3 through 283 or resid 288...	A	A	441 - 1527	441 - 1527
2	1	ALA	ALA	GLU	GLU	(chain B and resid 3 through 1527)	B	B	3 - 1527	3 - 1527

#1: Protein	4-alpha-glucanotransferase / Amylo-alpha-1 / 6-glucosidase / Dextrin 6-alpha-D-glucosidase / Glycogen debrancher / Glycogen ...Amylo-alpha-1 / 6-glucosidase / Dextrin 6-alpha-D-glucosidase / Glycogen debrancher / Glycogen debranching enzyme / Oligo-1 / 4-1 / 4-glucantransferase Mass: 175429.406 Da / Num. of mol.: 2 / Mutation: W958A Source method: isolated from a genetically manipulated source Source: (gene. exp.) [Candida] glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: GDB1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6FSK0, 4-alpha-glucanotransferase, amylo-alpha-1,6-glucosidase

#1: Protein

4-alpha-glucanotransferase / Amylo-alpha-1 / 6-glucosidase / Dextrin 6-alpha-D-glucosidase / Glycogen debrancher / Glycogen ...

Mass: 175429.406 Da / Num. of mol.: 2 / Mutation: W958A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

[Candida] glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: GDB1 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q6FSK0, 4-alpha-glucanotransferase, amylo-alpha-1,6-glucosidase

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 5000 MME,0.1 M Tris pH7.0,5% Tasimate pH7.0, 3.5mM TCEP hydrochiloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 3.1→46.8 Å / Num. obs: 75998 / % possible obs: 99.9 % / Redundancy: 7.402 % / B_iso Wilson estimate: 84.39 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.1 / R_rim(I) all: 0.107 / Χ²: 0.913 / Net I/σ(I): 15.39 / Num. measured all: 562556 / Scaling rejects: 70

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
3.1-3.18	7.555	0.95	1.95	42072	5569	5569	0.732	1.02	100
3.18-3.27	7.55	0.731	2.58	40833	5409	5408	0.821	0.784	100
3.27-3.36	7.555	0.546	3.45	39956	5289	5289	0.9	0.586	100
3.36-3.47	7.549	0.387	4.81	38992	5165	5165	0.945	0.416	100
3.47-3.58	7.536	0.299	6.23	37448	4969	4969	0.966	0.321	100
3.58-3.71	7.538	0.221	8.31	36046	4782	4782	0.983	0.237	100
3.71-3.85	7.507	0.179	10.34	34990	4661	4661	0.988	0.193	100
3.85-4	7.475	0.137	13.31	33729	4513	4512	0.992	0.147	100
4-4.18	7.441	0.107	16.61	31961	4295	4295	0.995	0.115	100
4.18-4.38	7.423	0.089	19.39	30538	4115	4114	0.997	0.096	100
4.38-4.62	7.381	0.077	22.52	29038	3934	3934	0.997	0.083	100
4.62-4.9	7.336	0.07	24.06	27259	3716	3716	0.997	0.075	100
4.9-5.24	7.285	0.066	25.72	25424	3490	3490	0.998	0.071	100
5.24-5.66	7.269	0.066	25.33	23864	3284	3283	0.997	0.071	100
5.66-6.2	7.136	0.063	26.26	21644	3033	3033	0.998	0.068	100
6.2-6.93	7.069	0.055	29.34	19256	2725	2724	0.998	0.059	100
6.93-8	7.278	0.045	33.63	17832	2450	2450	0.999	0.049	100
8-9.8	7.141	0.038	38.54	14690	2057	2057	0.999	0.041	100
9.8-13.86	6.97	0.034	40.36	11396	1635	1635	0.999	0.037	100
13.86-46.8	6.127	0.036	36.57	5588	962	912	0.997	0.039	94.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5d06

5d06

Resolution: 3.1→46.8 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2731	2713	3.57 %
R_work	0.2311	73222	-
obs	0.2326	75935	99.94 %

Solvent computation

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

Displacement parameters

B_iso max: 181.08 Å² / B_iso mean: 86.5856 Å² / B_iso min: 31.62 Å²

Refinement step

Cycle: final / Resolution: 3.1→46.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24309	0	0	0	24309
Num. residues	-	-	-	-	3023

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	13639	X-RAY DIFFRACTION	11.878	TORSIONAL
1	2	B	13639	X-RAY DIFFRACTION	11.878	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 19

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.1-3.16	0.4507	144	0.4221	3794	3938	100
3.16-3.22	0.3845	124	0.3694	3866	3990	100
3.22-3.28	0.3576	136	0.3099	3809	3945	100
3.28-3.35	0.329	163	0.2887	3788	3951	100
3.35-3.43	0.3135	137	0.2762	3812	3949	100
3.43-3.52	0.3517	139	0.2785	3819	3958	100
3.52-3.61	0.3336	142	0.2845	3840	3982	100
3.61-3.72	0.309	144	0.2872	3853	3997	100
3.72-3.84	0.2885	143	0.2654	3801	3944	100
3.84-3.98	0.2952	143	0.2374	3841	3984	100
3.98-4.14	0.2875	147	0.2239	3851	3998	100
4.14-4.32	0.2693	139	0.2172	3855	3994	100
4.32-4.55	0.2446	142	0.2133	3848	3990	100
4.55-4.84	0.263	143	0.1996	3851	3994	100
4.84-5.21	0.2421	141	0.1936	3860	4001	100
5.21-5.73	0.2589	148	0.2152	3882	4030	100
5.73-6.56	0.2697	143	0.2271	3890	4033	100
6.56-8.26	0.2448	145	0.214	3930	4075	100
8.26-46.8	0.2067	150	0.176	4032	4182	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	0.0089	-0.0099	-0.01	0.013	0.0062	0.0391	0.113	0.0377	0.1556	0.0007	0.1022	-0.0487	0.0238	0.0685	0.0002	0.3961	-0.0905	0.1449	0.4088	-0.0413	0.5436	38.2003	104.6975	173.373
2	0.071	0.0094	-0.0294	0.0592	-0.0227	0.0475	0.1958	-0.0625	-0.0017	-0.1027	-0.0972	0.0388	0.0843	0.2906	0	0.4301	0.0647	-0.0404	0.4786	-0.0349	0.2781	78.4161	100.211	216.6086
3	0.2176	-0.1271	-0.1826	0.3361	0.1688	0.2649	0.2078	-0.0428	0.34	-0.0194	0.0061	-0.1668	-0.3184	0.053	0.9031	0.4559	0.0209	0.319	0.1728	0.1534	0.4448	14.6298	119.154	168.6024
4	0.2133	0.0017	0.1172	0.0724	0.0712	0.1419	0.1751	-0.0467	-0.1113	-0.0409	-0.015	0.0187	0.2857	0.0578	0.0001	0.5821	-0.0096	-0.13	0.3843	0.0367	0.3486	55.951	83.5907	219.1079
5	0.2624	-0.0541	0.0704	0.2708	0.0928	0.3816	0.2296	0.1603	0.2022	0.0007	0.222	0.3323	-0.301	-0.2998	0.7741	0.6557	0.0728	0.2501	0.6482	0.2838	0.5946	26.6123	123.4825	127.3707
6	0.4005	-0.1218	-0.1876	0.5071	-0.153	0.5225	0.0142	-0.3177	-0.0523	0.3488	0.1573	-0.0458	-0.0056	-0.0026	0.8077	0.8674	0.0201	-0.1155	0.4714	0.2433	0.1683	69.3798	74.9748	258.5042
7	0.1213	-0.0229	-0.0769	0.0348	-0.0001	0.0539	0.0793	0.0412	-0.0051	0.0312	-0.1512	0.0488	-0.2098	-0.0453	-0	0.4364	0.0795	0.1305	0.5063	0.0387	0.5001	-7.6901	105.0447	173.8517
8	0.1597	0.0119	0.0602	0.0267	-0.0176	0.0364	0.1672	-0.1134	-0.0322	-0.0169	-0.1008	0.1854	0.0368	-0.1536	0.0001	0.4548	-0.1383	-0.0126	0.5532	0.0858	0.4865	32.6964	96.6862	215.5328
9	0.1572	0.1081	0.1218	0.1545	0.0506	0.1345	-0.2621	-0.0507	-0.1333	0.0972	0.1326	0.2292	0.0858	0.02	-0.0513	0.3875	0.0379	0.155	0.4063	0.0555	0.3322	19.4539	77.5574	185.8176
10	0.0795	0.0024	0.0063	0.0524	0.0179	0.0639	0.1241	-0.0096	0.2006	0.0333	-0.0166	0.1698	0.0085	-0.0482	-0	0.3638	0.0218	0.1044	0.3437	-0.0079	0.4521	57.3927	127.1134	207.6521
11	0.0739	-0.086	0.0499	0.3838	0.0775	0.3021	-0.2768	0.0096	-0.3434	0.0031	0.1383	-0.3309	0.1369	0.2925	-0.2287	0.2808	0.0908	0.2625	0.455	-0.0154	0.572	51.2	60.2131	175.5428
12	0.3377	0.0319	0.0217	0.1683	-0.0402	0.0786	0.2012	-0.2938	0.764	0.1461	-0.0838	-0.0962	-0.2416	0.1293	0.1657	0.4251	-0.1547	0.1091	0.485	-0.3715	0.6625	87.2675	145.5086	221.1043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and ((resseq 3:131))	A	3 - 131
2	X-RAY DIFFRACTION	2	chain 'B' and ((resseq 3:131))	B	3 - 131
3	X-RAY DIFFRACTION	3	chain 'A' and ((resseq 132:237) or (resseq 499:749))	A	0
4	X-RAY DIFFRACTION	4	chain 'B' and ((resseq 132:237) or (resseq 499:749))	B	0
5	X-RAY DIFFRACTION	5	chain 'A' and ((resseq 238:498))	A	238 - 498
6	X-RAY DIFFRACTION	6	chain 'B' and ((resseq 238:498))	B	238 - 498
7	X-RAY DIFFRACTION	7	chain 'A' and ((resseq 750:869))	A	750 - 869
8	X-RAY DIFFRACTION	8	chain 'B' and ((resseq 750:869))	B	750 - 869
9	X-RAY DIFFRACTION	9	chain 'A' and ((resseq 870:1022))	A	0
10	X-RAY DIFFRACTION	10	chain 'B' and ((resseq 870:1022))	B	0
11	X-RAY DIFFRACTION	11	chain 'A' and ((resseq 1023:1527))	A	0
12	X-RAY DIFFRACTION	12	chain 'B' and ((resseq 1023:1528))	B	0

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