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- PDB-5awp: Arthrobacter globiformis T6 isomalto-dextranase complexed with is... -

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Basic information

Entry
Database: PDB / ID: 5awp
TitleArthrobacter globiformis T6 isomalto-dextranase complexed with isomaltose
ComponentsIsomaltodextranase
KeywordsHYDROLASE / TIM barrel / glycoside hydrolase / GH27 / carbohydrate binding module / CBM35
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosyl hydrolase, all-beta ...Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Isomaltodextranase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTonozuka, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27
Authors: Okazawa, Y. / Miyazaki, T. / Yokoi, G. / Ishizaki, Y. / Nishikawa, A. / Tonozuka, T.
History
DepositionJul 8, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Structure summary
Revision 1.3Nov 11, 2015Group: Database references
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isomaltodextranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6734
Polymers66,8931
Non-polymers7803
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint11 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.708, 123.708, 84.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Isomaltodextranase


Mass: 66893.109 Da / Num. of mol.: 1 / Fragment: UNP residues 31-636
Source method: isolated from a genetically manipulated source
Details: The sequence for the mature enzyme "ATAV ... ELDM" (606 amino acid residues) was fused with N-terminal His-tag, and the expressed protein was digested with thrombin. Therefore, the first ...Details: The sequence for the mature enzyme "ATAV ... ELDM" (606 amino acid residues) was fused with N-terminal His-tag, and the expressed protein was digested with thrombin. Therefore, the first four N-terminal residues GSHM are derived from the expression plasmid pET28a.
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: g2d / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WSN5
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: PEG 8000, sodium acetate buffer, potassium dihydrogenphosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43201 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 40
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 13.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AWO

5awo


Resolution: 2→30.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.31 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19593 2178 5 %RANDOM
Rwork0.15702 ---
obs0.15901 40989 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.836 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 51 601 5286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194834
X-RAY DIFFRACTIONr_bond_other_d0.0010.024323
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9316601
X-RAY DIFFRACTIONr_angle_other_deg0.79439894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82523.504234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08415681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8681534
X-RAY DIFFRACTIONr_chiral_restr0.080.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.7862391
X-RAY DIFFRACTIONr_mcbond_other1.0841.7852390
X-RAY DIFFRACTIONr_mcangle_it1.7822.6722989
X-RAY DIFFRACTIONr_mcangle_other1.7822.6732990
X-RAY DIFFRACTIONr_scbond_it1.2491.8752442
X-RAY DIFFRACTIONr_scbond_other1.2471.8732438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0662.7683607
X-RAY DIFFRACTIONr_long_range_B_refined4.45715.3346259
X-RAY DIFFRACTIONr_long_range_B_other4.09814.8195929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 152 -
Rwork0.176 3013 -
obs--99.97 %

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