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- PDB-4j3u: Crystal structure of barley limit dextrinase in complex with malt... -

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Basic information

Entry
Database: PDB / ID: 4j3u
TitleCrystal structure of barley limit dextrinase in complex with maltosyl-S-betacyclodextrin
ComponentsLimit dextrinase
KeywordsHYDROLASE / GH13 hydrolase
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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Limit dextrinase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSim, L. / Windahl, M.S. / Moeller, M.S. / Henriksen, A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase
Authors: Moeller, M.S. / Windahl, M.S. / Sim, L. / Bjstrup, M. / Abou Hachem, M. / Hindsgaul, O. / Palcic, M. / Svensson, B. / Henriksen, A.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2May 30, 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 / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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_alt_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Limit dextrinase
B: Limit dextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,77242
Polymers199,4932
Non-polymers7,27940
Water29,0401612
1
A: Limit dextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,89425
Polymers99,7471
Non-polymers4,14724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Limit dextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87917
Polymers99,7471
Non-polymers3,13216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)195.430, 84.610, 121.790
Angle α, β, γ (deg.)90.00, 119.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Limit dextrinase


Mass: 99746.727 Da / Num. of mol.: 2 / Fragment: UNP Residues 22-905
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FYY0, pullulanase
#2: Polysaccharide Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-1)]6-thio-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1493.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,9,9/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g6-h1*S*_h4-i1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 1650 molecules

#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1612 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHESE RESIDUES REPRESENT NATURAL VARIANTS.

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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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.3M NaI, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 188337 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.896 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.6830.5152.6311137330503300590.60298.5
1.8-1.930.4040.3094.2610742328650285400.36199.6
1.93-2.080.2450.1926.6110018426647265130.22499.5
2.08-2.280.1490.1239.939265924576244680.14399.6
2.28-2.540.10.08713.378463122311222250.10199.6
2.54-2.930.0660.06117.87458819661195650.07199.5
2.93-3.580.0410.04323.666295216713166200.05199.4
3.58-5.030.0340.03926.564874613051129670.04699.4
5.030.0350.03926.4527274753573800.04597.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y4S

2y4s


Resolution: 1.7→29.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2046 / WRfactor Rwork: 0.1632 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8562 / SU B: 5.072 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1843 / SU Rfree: 0.1109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 9417 5 %RANDOM
Rwork0.1723 ---
obs0.1746 188323 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.36 Å2 / Biso mean: 20.029 Å2 / Biso min: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.02 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13465 0 236 1612 15313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01914115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212944
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.96419251
X-RAY DIFFRACTIONr_angle_other_deg0.742329864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53651762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34824.028653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.717152190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.751588
X-RAY DIFFRACTIONr_chiral_restr0.060.22152
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023281
X-RAY DIFFRACTIONr_rigid_bond_restr1.802327059
X-RAY DIFFRACTIONr_sphericity_free29.3235523
X-RAY DIFFRACTIONr_sphericity_bonded6.623527823
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 684 -
Rwork0.226 12998 -
all-13682 -
obs--98.23 %

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