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

ID or keywords:

Entry

Database: PDB / ID: 7ekw

Title

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (D535N) in complex with maltotetrose

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: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of glycogen-debranching enzyme mutants in complex with oligosaccharides.
Authors: Shen, M. / Gong, X. / Xiang, S.

History

Deposition	Apr 7, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ekw.cif.gz	1.2 MB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	7ekw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7ekw_validation.pdf.gz	780.9 KB	Display	wwPDB validaton report
Full document	7ekw_full_validation.pdf.gz	839.3 KB	Display
Data in XML	7ekw_validation.xml.gz	101.2 KB	Display
Data in CIF	7ekw_validation.cif.gz	134.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ek/7ekw ftp://data.pdbj.org/pub/pdb/validation_reports/ek/7ekw	HTTPS FTP

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Related structure data

Related structure data	7eimC 7ejpC 7ejtC 7ekxC 5d0fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ekx-d 7ejt-d 7eim-d 7ejp-d 5d0f-d 6014 5ipq-d 21312 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	#74 - Feb 2006 alpha-Amylase similarity (2)

Deposited unit

A: 4-alpha-glucanotransferase

B: 4-alpha-glucanotransferase

hetero molecules

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)	160.250, 198.940, 134.590
Angle α, β, γ (deg.)	90.000, 104.870, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein

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

Mass: 175543.547 Da / Num. of mol.: 2 / Mutation: D535N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Candida glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: GDB1, CAGL0G09977g / Production host:

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

#2: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically

Has ligand of interest

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: 2.97 Å³/Da / Density % sol: 58.6 %
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: 0.97939 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97939 Å / Relative weight: 1
Reflection	Resolution: 3.1→25.75 Å / Num. obs: 73585 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC_1/2: 0.991 / Net I/σ(I): 6.7
Reflection shell	Resolution: 3.1→3.27 Å / Num. unique obs: 10713 / CC_1/2: 0.564 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.27	data extraction
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5D0F

5d0f

Resolution: 3.1→25.26 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2718	3764	5.13 %
R_work	0.248	69640	-
obs	0.2493	73404	99.73 %

Solvent computation

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

Displacement parameters

B_iso max: 217.62 Å² / B_iso mean: 101.9921 Å² / B_iso min: 41.16 Å²

Refinement step

Cycle: final / Resolution: 3.1→25.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24507	0	23	0	24530
B_iso mean	-	-	116.11	-	-
Num. residues	-	-	-	-	3046

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.1-3.14	0.3931	143	0.3892	2571	2714	100
3.14-3.18	0.4182	133	0.3848	2557	2690	100
3.18-3.22	0.3711	149	0.3714	2571	2720	100
3.22-3.27	0.3654	122	0.3685	2616	2738	100
3.27-3.32	0.3712	135	0.3514	2551	2686	100
3.32-3.37	0.352	133	0.3314	2584	2717	100
3.37-3.43	0.3616	145	0.3346	2537	2682	100
3.43-3.48	0.3085	117	0.3234	2618	2735	100
3.48-3.55	0.3397	133	0.3156	2627	2760	100
3.55-3.62	0.3153	138	0.3032	2537	2675	100
3.62-3.69	0.326	133	0.2881	2581	2714	100
3.69-3.77	0.2921	138	0.2852	2590	2728	100
3.77-3.86	0.3056	134	0.2787	2592	2726	100
3.86-3.95	0.2949	114	0.2616	2581	2695	100
3.95-4.06	0.2613	143	0.2651	2584	2727	100
4.06-4.18	0.2492	155	0.2417	2536	2691	100
4.18-4.31	0.2385	160	0.2374	2568	2728	100
4.31-4.47	0.2603	131	0.2295	2586	2717	100
4.47-4.64	0.272	149	0.2211	2592	2741	100
4.64-4.85	0.2529	132	0.2266	2588	2720	100
4.85-5.11	0.2681	149	0.2129	2582	2731	100
5.11-5.42	0.2622	131	0.2146	2579	2710	100
5.42-5.84	0.2597	167	0.2309	2578	2745	100
5.84-6.42	0.2636	139	0.2364	2584	2723	99
6.42-7.33	0.2307	150	0.2223	2542	2692	99
7.33-9.15	0.2261	156	0.1807	2576	2732	99
9.16-25.26	0.1923	135	0.1732	2632	2767	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	2.347	-0.4958	-0.1502	3.0653	-0.2962	1.4562	0.1101	-0.4401	-0.4455	0.0091	0.116	0.525	0.412	-0.6592	-0.0295	0.7268	-0.2537	-0.0675	0.9537	0.0231	0.8391	-56.646	4.637	45.119
2	2.1515	-1.1174	-0.3631	3.408	0.7901	2.672	0.3562	-0.0308	0.743	-0.254	0.0742	-0.5351	-0.1193	0.663	-0.3056	0.6455	0.0786	0.1583	0.9055	-0.1159	0.9753	-100.116	10.573	41.858
3	2.5981	-0.4682	0.2548	1.7922	-0.1115	1.0938	0.1098	-0.0602	-0.8967	-0.1181	-0.0279	-0.0462	0.7431	-0.0589	0.0125	0.8779	-0.0695	-0.0425	0.5233	-0.0987	0.7271	-33.37	-10.31	39.688
4	3.2319	-1.2279	0.0837	2.648	0.1735	0.9782	0.2697	0.2279	1.009	-0.2213	-0.1083	-0.6175	-0.3864	0.1239	-0.0683	0.7111	0.0816	0.2591	0.5806	-0.0044	0.8134	-123.387	26.234	38.487
5	2.7703	1.7058	0.544	1.5606	-0.7979	2.0292	-0.2251	0.7979	-0.097	-1.4378	0.1418	-0.1822	0.2459	0.0812	0.1403	2.2246	-0.0072	0.0641	0.8329	-0.4231	0.9474	-47.573	-15.542	-0.22
6	1.1371	-0.064	-1.6056	0.2075	0.7548	2.4665	0.1093	0.7904	-0.1728	-0.4208	-0.0758	0.191	-0.4181	-0.4362	0.2777	1.6397	0.2774	0.3017	1.4955	0.2223	1.4353	-112.758	32.538	-2.552
7	4.3304	1.0896	0.8358	2.8419	0.3876	1.7569	-0.0217	-0.2284	-0.0687	-0.0977	-0.047	-0.3358	0.3661	0.1215	0.0885	0.6912	0.1	-0.0041	0.6493	0.0087	0.8544	-10.625	3.843	43.484
8	2.9142	0.5777	-0.9228	3.5309	-0.4731	1.7366	0.0467	-0.2081	-0.2928	-0.0408	-0.0951	0.1237	0.0179	-0.0331	-0.006	0.6926	0.232	0.1308	0.6886	0.0168	0.7344	-146.114	12.418	42.825
9	2.7801	-0.0285	0.3	3.3626	-0.903	2.4148	-0.2518	-0.3858	0.3844	0.7904	-0.0194	-0.8219	-0.2827	-0.2896	0.127	0.6324	0.0398	-0.2332	0.6386	-0.1952	0.5565	-36.976	31.718	56.599
10	4.0106	-0.3301	0.4321	2.7691	-0.4679	3.2292	0.4404	0.3298	-0.8599	-0.0388	0.0264	0.4347	-0.0084	-0.621	-0.3294	0.5074	0.1921	-0.0947	0.6014	-0.0111	0.5877	-120.361	-16.894	51.497
11	2.9317	-0.1122	0.6946	4.2269	0.1707	3.1782	-0.2318	-0.0653	0.818	-0.2287	0.0716	1.7148	-0.5998	-1.1348	-0.1729	0.348	0.4782	-0.1641	0.873	-0.3219	0.956	-68.993	49.336	47.397
12	4.3423	-0.4669	-0.0694	2.4914	-0.6036	2.6334	0.623	0.9826	-1.7316	-0.4205	-0.4631	-0.0945	0.4137	0.0258	0.2213	0.5641	0.3765	-0.1912	0.6044	-0.687	1.0969	-89.527	-34.692	38.915

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 RESID 3:131 )	A	3 - 131
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 3:131 )	B	3 - 131
3	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 132:237 OR RESID 499:749 ) )	A	132 - 237
4	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 132:237 OR RESID 499:749 ) )	A	499 - 749
5	X-RAY DIFFRACTION	4	( CHAIN B AND ( RESID 132:237 OR RESID 499:749 ) )	B	132 - 237
6	X-RAY DIFFRACTION	4	( CHAIN B AND ( RESID 132:237 OR RESID 499:749 ) )	B	499 - 749
7	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 238:498 )	A	238 - 498
8	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 238:498 )	B	238 - 498
9	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 750:869 )	A	750 - 869
10	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 750:869 )	B	750 - 869
11	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 870:1022 )	A	870 - 1022
12	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 870:1022 )	B	870 - 1022
13	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 1023:1528 )	A	1023 - 1528
14	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 1023:1528 )	B	1023 - 1528

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