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- PDB-2y5e: BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN -

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Basic information

Entry
Database: PDB / ID: 2y5e
TitleBARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN
ComponentsLIMIT DEXTRINASE
KeywordsHYDROLASE / STARCH / PULLULANASE / DEBRANCHING ENZYME / GLYCOSIDE HYDROLASE 13
Function / homology
Function and homology information


pullulanase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-cyclodextrin / IODIDE ION / Limit dextrinase
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsVester-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.
#1: Journal: Protein Expr.Purif. / Year: 2010
Title: Secretory Expression of Functional Barley Limit Dextrinase by Pichia Pastoris Using High Cell- Density Fermentation.
Authors: Vester-Christensen, M.B. / Hachem, M.A. / Naested, H. / Svensson, B.
History
DepositionJan 13, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionJan 26, 2011ID: 2X4C
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Non-polymer description
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _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 2.1Dec 20, 2023Group: 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 ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIMIT DEXTRINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,62213
Polymers97,4441
Non-polymers2,17812
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.840, 85.610, 61.120
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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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, pullulanase
#2: Polysaccharide Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 229 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / 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.: 8 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 102 TO ARG
Sequence details4 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6.6 / Details: 30% (W/V) PEG 3350, 0.3 M NAI, pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.03908
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 2.48→35.9 Å / Num. obs: 30821 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X4B

2x4b
PDB Unreleased entry


Resolution: 2.49→33.468 Å / SU ML: 0.3 / σ(F): 0.01 / Phase error: 16.19 / Stereochemistry target values: ML
Details: DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL. LAST REFINEMENT ROUND DID NOT INCLUDE RFREE.
RfactorNum. reflection% reflection
Rfree0.226 1532 5 %
Rwork0.1752 --
obs0.1752 30660 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.53 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.8696 Å20 Å24.8937 Å2
2---2.3125 Å20 Å2
3---5.1821 Å2
Refinement stepCycle: LAST / Resolution: 2.49→33.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6685 0 82 218 6985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026926
X-RAY DIFFRACTIONf_angle_d0.6479429
X-RAY DIFFRACTIONf_dihedral_angle_d18.4242546
X-RAY DIFFRACTIONf_chiral_restr0.0441014
X-RAY DIFFRACTIONf_plane_restr0.0021227
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4865-2.514800.29611029X-RAY DIFFRACTION49
2.5148-2.544300.27521755X-RAY DIFFRACTION85
2.5443-2.575400.25151715X-RAY DIFFRACTION85
2.5754-2.60800.23811816X-RAY DIFFRACTION87
2.608-2.642300.2371761X-RAY DIFFRACTION86
2.6423-2.678400.23351794X-RAY DIFFRACTION86
2.6784-2.716700.23191826X-RAY DIFFRACTION88
2.7167-2.757200.22021833X-RAY DIFFRACTION89
2.7572-2.800300.21671828X-RAY DIFFRACTION88
2.8003-2.846200.2121884X-RAY DIFFRACTION91
2.8462-2.895200.20281795X-RAY DIFFRACTION90
2.8952-2.947800.19952003X-RAY DIFFRACTION95
2.9478-3.004500.20171887X-RAY DIFFRACTION93
3.0045-3.065800.2111935X-RAY DIFFRACTION94
3.0658-3.132400.21141992X-RAY DIFFRACTION96
3.1324-3.205200.19752002X-RAY DIFFRACTION97
3.2052-3.285300.19191987X-RAY DIFFRACTION97
3.2853-3.37400.17152038X-RAY DIFFRACTION99
3.374-3.473200.16432031X-RAY DIFFRACTION98
3.4732-3.585200.15262006X-RAY DIFFRACTION98
3.5852-3.713200.15962026X-RAY DIFFRACTION98
3.7132-3.861700.14132049X-RAY DIFFRACTION99
3.8617-4.037100.12562080X-RAY DIFFRACTION99
4.0371-4.249600.12712015X-RAY DIFFRACTION99
4.2496-4.515200.12262052X-RAY DIFFRACTION99
4.5152-4.862900.12412043X-RAY DIFFRACTION99
4.8629-5.350500.12952058X-RAY DIFFRACTION99
5.3505-6.120600.16012070X-RAY DIFFRACTION99
6.1206-7.695800.17082038X-RAY DIFFRACTION100
7.6958-33.471400.16752045X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.76820.9068-0.73011.4056-0.4011.0205-0.040.59130.2947-0.10340.14550.56350.0218-0.5077-0.08540.2739-0.0427-0.05150.6180.01070.419814.99132.6068.0715
21.88821.4216-1.61281.2596-0.64783.3174-0.01381.10680.71170.1610.48550.31550.2302-0.5544-0.28020.2823-0.22130.00270.6982-0.02450.408614.5491-4.73291.1845
30.65940.249-0.32340.5826-0.19060.5363-0.0892-0.00950.00590.15390.08270.1885-0.0362-0.08770.00930.1348-0.00280.04230.0687-0.03320.239624.3457-2.387532.4716
41.43810.61620.73030.29820.18663.83490.0113-0.2964-0.12090.24160.05950.39080.4471-0.57950.010.2227-0.00210.1050.1391-0.00580.32923.6086-4.579238.4057
50.7343-0.22360.44690.1961-0.30490.5143-0.0939-0.0243-0.37950.06380.20390.1374-0.1571-0.012-0.09840.2411-0.04050.08430.1114-0.08560.271833.0688-7.415433.5164
60.7955-0.20540.06970.2451-0.14840.85490.078-0.1137-0.00250.16-0.05340.0361-0.04010.2153-0.02650.1674-0.0075-0.02220.106-0.00830.116760.6856-2.842434.4642
70.6171-0.2644-0.52730.3195-0.00170.7685-0.16760.0974-0.17380.10330.06810.09370.3130.04140.03220.20730.04290.01360.0638-0.01440.114955.6954-10.761229.1244
80.9353-0.0163-0.2990.12210.16360.5881-0.0693-0.0359-0.32910.0796-0.1110.10980.12660.17360.14470.18820.04080.03880.0016-0.04880.191353.2643-12.435128.4945
90.94740.0702-0.37350.3603-0.19140.3951-0.0220.10820.03570.11320.00810.0109-0.0024-0.0302-0.01710.12180.00530.01730.0741-0.03170.141840.25122.772421.2107
101.15040.50490.31890.26110.12251.14070.00660.17780.2019-0.21770.01190.08140.11040.1147-0.01130.1603-0.02280.00670.08850.01640.086749.85488.65499.08
110.3128-0.00590.23310.467-0.30960.578-0.0620.2995-0.13130.0089-0.18050.0040.110.0236-0.01370.1660.00290.07030.312-0.07510.122769.495-0.6546-2.1666
120.8670.1512-0.91710.3464-0.12641.1715-0.09970.3750.1235-0.00040.1769-0.03240.1813-0.1693-0.04580.1615-0.07290.00290.27720.02050.154561.1615.41474.2065
130.67860.0013-0.47630.58670.0871.0093-0.06940.163-0.0908-0.0338-0.0224-0.15240.14340.26390.05150.12910.06050.01690.1783-0.03470.177669.0831-7.702615.666
141.5461-0.0612-0.34650.7394-0.03350.48970.17370.36330.3511-0.0545-0.0419-0.263-0.26090.0317-0.07940.2341-0.07840.02480.25390.0580.318573.468122.656612.2416
150.12670.16860.10480.84460.01010.56410.08340.0072-0.103-0.0201-0.1872-0.3240.01290.33320.08160.114-0.0804-0.02820.37970.0460.259685.002613.206613.5424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:101)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 102:113)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 114:167)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 168:194)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 195:237)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 238:293)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 294:328)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 329:398)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 399:518)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 519:546)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 547:591)
12X-RAY DIFFRACTION12CHAIN A AND (RESSEQ 592:636)
13X-RAY DIFFRACTION13CHAIN A AND (RESSEQ 637:773)
14X-RAY DIFFRACTION14CHAIN A AND (RESSEQ 774:817)
15X-RAY DIFFRACTION15CHAIN A AND (RESSEQ 818:885)

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