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- PDB-4j3w: Crystal structure of barley limit dextrinase (E510A mutant) in co... -

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Basic information

Entry
Database: PDB / ID: 4j3w
TitleCrystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltohexasaccharide
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 / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / 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: 1.67 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 / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_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 / _pdbx_struct_special_symmetry.label_asym_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,73511
Polymers99,6891
Non-polymers2,04610
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.850, 80.940, 58.290
Angle α, β, γ (deg.)90.000, 100.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-913-

IOD

21A-1300-

HOH

31A-1315-

HOH

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Components

#1: Protein Limit dextrinase


Mass: 99688.688 Da / Num. of mol.: 1 / Fragment: UNP Residues 22-905 / Mutation: E510A
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 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-6[DGlcpa1-4]DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_b6-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.32 % / Mosaicity: 0.59 °
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: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.666→82.924 Å / Num. all: 89214 / Num. obs: 89214 / % possible obs: 97 % / Redundancy: 4.7 % / Rsym value: 0.079 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.65-1.7440.4050.3522.242726106490.1960.4050.3523.779.5
1.74-1.854.80.2660.2363.260377126980.1210.2660.2365.8100
1.85-1.984.80.1740.1554.656731118810.0790.1740.1558.2100
1.98-2.144.80.1280.1145.953202110770.0570.1280.11410.9100
2.14-2.344.80.1020.0916.849275102280.0450.1020.09113.4100
2.34-2.624.80.0840.0757.74478192540.0370.0840.07515.3100
2.62-3.024.90.0710.0638.33967181780.0310.0710.06317.6100
3.02-3.74.90.0620.0558.93356869120.0270.0620.05520.2100
3.7-5.234.80.0690.0628.32610153830.0310.0690.06221.7100
5.23-22.8254.70.0620.05691390529540.0270.0620.05620.598.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y4S

2y4s


Resolution: 1.67→22.83 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1878 / WRfactor Rwork: 0.1573 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9124 / SU B: 3.484 / SU ML: 0.054 / SU R Cruickshank DPI: 0.1545 / SU Rfree: 0.0896 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 4472 5 %RANDOM
Rwork0.1526 ---
obs0.154 89211 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.44 Å2 / Biso mean: 16.0249 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20.06 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.67→22.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6674 0 76 375 7125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026963
X-RAY DIFFRACTIONr_bond_other_d0.0020.026388
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9579494
X-RAY DIFFRACTIONr_angle_other_deg0.7973.00514702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68623.875320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.262151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.091544
X-RAY DIFFRACTIONr_chiral_restr0.0690.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021638
X-RAY DIFFRACTIONr_rigid_bond_restr1.065313345
X-RAY DIFFRACTIONr_sphericity_free15.7015102
X-RAY DIFFRACTIONr_sphericity_bonded2.94513457
LS refinement shellResolution: 1.666→1.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 287 -
Rwork0.236 5588 -
all-5875 -
obs--89.74 %

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