PDB-2y4s: BARLEY LIMIT DEXTRINASE IN COMPLEX WITH BETA-CYCLODEXTRIN

ID or keywords:

Entry

Database: PDB / ID: 2y4s

Title

BARLEY LIMIT DEXTRINASE IN COMPLEX WITH BETA-CYCLODEXTRIN

Components

LIMIT DEXTRINASE

Keywords

HYDROLASE / STARCH / PULLULANASE / DEBRANCHING ENZYME / GLYCOSIDE HYDROLASE FAMILY 13

Function / homology

Function and homology information

pullulanase / pullulanase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function

Biological species

HORDEUM VULGARE (barley)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Vester-Christensen, M.B. / Hachem, M.A. / Svensson, B. / Henriksen, A.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of an Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins.
Authors: Vester-Christensen, M.B. / Abou Hachem, M. / Svensson, B. / Henriksen, A.

History

Deposition	Jan 10, 2011	Deposition site: PDBE / Processing site: PDBE
Supersession	Jan 19, 2011	ID: 2X4B
Revision 1.0	Jan 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 21, 2012	Group: Database references / Non-polymer description / Source and taxonomy
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y4s.cif.gz	350.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2y4s.ent.gz	283.8 KB	Display	PDB format
PDBx/mmJSON format	2y4s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2y4s_validation.pdf.gz	981 KB	Display	wwPDB validaton report
Full document	2y4s_full_validation.pdf.gz	991.9 KB	Display
Data in XML	2y4s_validation.xml.gz	37.5 KB	Display
Data in CIF	2y4s_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4s ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4s	HTTPS FTP

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Related structure data

Related structure data	2y5eC 2fgzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4j3t-d 4j3w-d 4j3u-1 4j3s-d 2y5e-d 4j3v-d 4u8f-1 2kz7-d 1h81-1 2olc-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	#155 - Nov 2012 Vitamin D Receptor similarity (1)

Deposited unit

A: LIMIT DEXTRINASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	175.030, 82.390, 59.380
Angle α, β, γ (deg.)	90.00, 96.13, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein

LIMIT DEXTRINASE

Mass: 97444.156 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-904 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HORDEUM VULGARE (barley) / Production host:

PICHIA PASTORIS (fungus) / Strain (production host): GS115
References: UniProt: O48541, UniProt: Q9S7S8*PLUS, pullulanase

#2: Polysaccharide

Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin

Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin

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Non-polymers , 4 types, 574 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	ENGINEERED RESIDUE IN CHAIN A, LYS 102 TO ARG
Sequence details	4 AMINO ACID DISCREPANCIES. THE SEQUENCE STRETCH BETWEEN RESIDUES 484-486 REFLECTS THAT THE CLONED ...4 AMINO ACID DISCREPANCIES. THE SEQUENCE STRETCH BETWEEN RESIDUES 484-486 REFLECTS THAT THE CLONED CDNA IS FROM AN OFFSPRING OF THE UNP O48541 SOURCE AND THEREFORE A NATURAL VARIETY

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.5 % / Description: NONE
Crystal grow	pH: 6.6 / Details: pH 6.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 18, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.1→41.2 Å / Num. obs: 48879 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / B_iso Wilson estimate: 11.68 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FGZ

2fgz

Resolution: 2.1→41.195 Å / SU ML: 0.18 / σ(F): 0.01 / Phase error: 13.62 / Stereochemistry target values: ML
Details: DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL. LAST REFINEMENT ROUND DID NOT INCLUDE RFREE.

	R_factor	Num. reflection	% reflection
R_free	0.204	2447	5 %
R_work	0.1654	-	-
obs	0.1654	48246	95.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.121 Å² / k_sol: 0.41 e/Å³

Displacement parameters

B_iso mean: 16.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.5442 Å²	0 Å²	1.8378 Å²
2-	-	-0.5497 Å²	0 Å²
3-	-	-	2.0939 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→41.195 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6650	0	126	560	7336

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6969
X-RAY DIFFRACTION	f_angle_d	0.784	9490
X-RAY DIFFRACTION	f_dihedral_angle_d	21.32	2573
X-RAY DIFFRACTION	f_chiral_restr	0.052	1019
X-RAY DIFFRACTION	f_plane_restr	0.002	1229

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.1239	0.215	2865	X-RAY DIFFRACTION	88
2.1239-2.1489	0.2148	2851	X-RAY DIFFRACTION	89
2.1489-2.1751	0.1977	2810	X-RAY DIFFRACTION	89
2.1751-2.2026	0.1884	3000	X-RAY DIFFRACTION	91
2.2026-2.2316	0.1841	2860	X-RAY DIFFRACTION	90
2.2316-2.2622	0.1763	2973	X-RAY DIFFRACTION	92
2.2622-2.2945	0.1744	2948	X-RAY DIFFRACTION	92
2.2945-2.3287	0.1718	2936	X-RAY DIFFRACTION	93
2.3287-2.3651	0.1682	3068	X-RAY DIFFRACTION	92
2.3651-2.4039	0.1694	2985	X-RAY DIFFRACTION	95
2.4039-2.4453	0.167	2961	X-RAY DIFFRACTION	93
2.4453-2.4898	0.1667	3047	X-RAY DIFFRACTION	94
2.4898-2.5377	0.1602	3080	X-RAY DIFFRACTION	95
2.5377-2.5895	0.1488	3032	X-RAY DIFFRACTION	95
2.5895-2.6458	0.151	3064	X-RAY DIFFRACTION	96
2.6458-2.7073	0.1559	3086	X-RAY DIFFRACTION	96
2.7073-2.775	0.1409	3064	X-RAY DIFFRACTION	96
2.775-2.85	0.1445	3130	X-RAY DIFFRACTION	97
2.85-2.9338	0.1454	3121	X-RAY DIFFRACTION	97
2.9338-3.0285	0.1348	3129	X-RAY DIFFRACTION	98
3.0285-3.1367	0.1332	3141	X-RAY DIFFRACTION	98
3.1367-3.2622	0.1432	3100	X-RAY DIFFRACTION	98
3.2622-3.4106	0.1386	3185	X-RAY DIFFRACTION	99
3.4106-3.5904	0.1391	3214	X-RAY DIFFRACTION	99
3.5904-3.8152	0.1429	3168	X-RAY DIFFRACTION	99
3.8152-4.1095	0.1454	3174	X-RAY DIFFRACTION	99
4.1095-4.5226	0.1524	3216	X-RAY DIFFRACTION	100
4.5226-5.1759	0.1724	3199	X-RAY DIFFRACTION	100
5.1759-6.5169	0.2071	3191	X-RAY DIFFRACTION	100
6.5169-41.203	0.2193	3187	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	0.1928	0.0523	-0.228	0.0931	-0.0962	0.2873	-0.0438	0.0784	0.0845	-0.0309	0.0901	0.0282	0.0916	-0.1794	-0.0477	0.1185	-0.062	-0.1004	0.1799	0.0513	0.1433	13.0511	41.2942	36.8578
2	0.6363	-0.2491	-0.4836	0.1549	0.1771	0.3789	0.0003	-0.0584	-0.0012	-0.0691	0.0827	-0.0176	-0.1848	0.3072	-0.0829	0.4615	-0.2227	-0.0042	0.5629	-0.0156	0.2866	3.4366	31.3093	36.7636
3	0.1475	0.192	-0.3624	0.332	-0.4341	0.91	-0.0943	0.2132	0.1915	-0.0666	0.2412	0.1843	0.0288	-0.4588	-0.1625	0.0625	-0.063	-0.0865	0.2613	0.1224	0.1764	13.331	47.8742	36.743
4	0.3455	0.1259	-0.0772	0.0603	-0.0168	0.0269	-0.0182	0.0032	0.0596	0.0094	0.0057	0.0398	0.0063	-0.008	-0.0001	-0.0231	-0.0095	0.0259	-0.003	-0.016	0.0662	21.3484	41.0986	64.2111
5	0.1738	0.0732	-0.0393	0.1284	0.0815	0.1456	0.0141	0.0131	0.0635	-0.0069	0.0457	-0.0432	0.0228	-0.0234	-0.055	0.0234	-0.0303	0.0041	0.0169	-0.0026	0.0913	26.8139	35.051	60.9055
6	0.08	0.0389	0.0069	0.0341	0.0701	0.278	0.0334	-0.0553	0.0388	0.0291	-0.0285	0.019	0.0297	0.0019	-0.0035	0.0203	-0.0262	0.02	0.0263	-0.0468	0.0107	54.7333	45.5463	63.4573
7	0.9026	0.4812	0.0702	0.9864	0.2076	0.0451	0.0595	-0.1829	-0.0162	0.2194	-0.0215	-0.0614	0.0522	0.0481	-0.0371	0.0508	0.0025	-0.0168	0.0704	-0.0058	-0.0003	59.6077	34.3242	66.9881
8	0.4914	0.0384	-0.2741	0.0313	0.0368	0.2814	-0.087	0.0165	-0.1385	0.0263	-0.0011	-0.0108	0.1022	-0.0048	0.0655	0.0297	0.0081	0.0116	-0.0436	-0.0207	0.0244	50.3356	28.1749	56.461
9	0.127	0.1333	0.0044	0.1902	-0.038	0.0415	-0.0088	0.0064	0.0498	-0.0266	0.0325	0.0673	0.0168	-0.0094	0.0146	-0.0324	-0.0499	-0.0168	-0.0448	-0.0352	-0.0005	39.6165	46.2511	51.258
10	0.8147	0.1562	-0.1781	0.1228	-0.0021	0.0496	-0.1	0.1168	-0.0173	-0.042	0.0634	-0.0018	0.022	-0.0267	0.0433	0.0312	-0.0259	0.0065	0.0016	-0.0124	-0.0178	61.1422	43.1705	34.226
11	2.0167	0.673	0.6822	1.4612	0.5963	0.3417	-0.2343	0.4207	-0.0798	-0.4834	0.0892	0.0572	-0.3798	0.0245	0.1418	0.2143	-0.0392	0.0077	0.1595	-0.0479	0.0342	69.1294	38.2932	21.2618
12	0.9758	0.0627	-0.2141	0.1698	-0.2801	0.4748	0.0023	0.3067	0.1395	-0.0304	0.028	0.0038	0.0648	-0.0918	-0.0176	0.0232	-0.0075	0.0166	0.0867	0.0499	0.0187	63.3736	56.339	29.994
13	0.1285	-0.0197	-0.1431	0.0595	0.0379	0.2431	-0.0779	0.0091	-0.0529	-0.009	0.0153	-0.0187	0.0808	0.024	-0.005	0.0024	0.0093	0.0228	-0.019	-0.0626	-0.014	64.4257	36.8947	43.9636
14	1.0513	0.0612	-0.1989	0.0057	-0.0321	0.2477	-0.0115	0.0915	0.1502	-0.0284	0.0197	-0.0076	-0.0449	0.0255	-0.0424	0.0087	-0.0198	0.0222	0.0123	0.0077	0.0245	72.7577	61.4985	41.0763
15	0.233	0.3192	-0.1386	0.5653	-0.1188	0.1214	0.0277	-0.1064	-0.0532	-0.0144	-0.0218	-0.1427	-0.0354	0.0866	-0.0043	0.0203	-0.0339	0.0107	0.0794	-0.0122	0.0457	83.3063	56.157	44.4296

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 3:40)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 41:51)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 52:113)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 114:190)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 191:231)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 232:269)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 270:294)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 295:378)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 379:531)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESSEQ 532:569)
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESSEQ 570:581)
12	X-RAY DIFFRACTION	12	CHAIN A AND (RESSEQ 582:613)
13	X-RAY DIFFRACTION	13	CHAIN A AND (RESSEQ 614:767)
14	X-RAY DIFFRACTION	14	CHAIN A AND (RESSEQ 768:835)
15	X-RAY DIFFRACTION	15	CHAIN A AND (RESSEQ 836:885)

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Yorodumi