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- PDB-5x7r: Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltra... -

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Basic information

Entry
Database: PDB / ID: 5x7r
TitleCrystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase complexed with isomaltohexaose
ComponentsGlycoside hydrolase family 31 alpha-glucosidase
KeywordsHYDROLASE / TRANSFERASE / glydoside hydrolase family 31 / carbohydrate-binding module family 35 / carbohydrate-binding module family 61
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Domain of unknown function DUF5110 / Carbohydrate binding module (family 35) / Domain of unknown function (DUF5110) / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 ...: / Domain of unknown function DUF5110 / Carbohydrate binding module (family 35) / Domain of unknown function (DUF5110) / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltose / acarbose-derived trisaccharide / beta-D-glucopyranose / alpha-D-glucopyranose / NICKEL (II) ION / Glycoside hydrolase family 31 alpha-glucosidase
Similarity search - Component
Biological speciesPaenibacillus sp. 598K (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFujimoto, Z. / Kishine, N. / Suzuki, N. / Momma, M. / Ichinose, H. / Kimura, A. / Funane, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
MAFFA25001 Japan
Citation
Journal: Biochem. J. / Year: 2017
Title: Carbohydrate-binding architecture of the multi-modular alpha-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces alpha-1,6-glucosyl-alpha-glucosaccharides from starch
Authors: Fujimoto, Z. / Suzuki, N. / Kishine, N. / Ichinose, H. / Momma, M. / Kimura, A. / Funane, K.
#1: Journal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: Paenibacillus sp. 598K 6-alpha-glucosyltransferase is essential for cycloisomaltooligosaccharide synthesis from alpha-(1 -> 4)-glucan
Authors: Ichinose, H. / Suzuki, R. / Miyazaki, T. / Kimura, K. / Momma, M. / Suzuki, N. / Fujimoto, Z. / Kimura, A. / Funane, K.
History
DepositionFeb 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / 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.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 31 alpha-glucosidase
B: Glycoside hydrolase family 31 alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,69783
Polymers275,3682
Non-polymers10,32881
Water29,7611652
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46610 Å2
ΔGint-354 kcal/mol
Surface area79250 Å2
Unit cell
Length a, b, c (Å)184.333, 271.260, 133.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2746-

HOH

21B-2802-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 31 alpha-glucosidase / alpha-1 / 6-glucosyltransferase / alpha-glucosidase


Mass: 137684.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. 598K (bacteria) / Strain: 598K / Gene: 6gt31a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A193PKW5, Transferases; Glycosyltransferases; Hexosyltransferases, alpha-glucosidase

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Sugars , 6 types, 11 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2/a6-b1_b6-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / acarbose-derived trisaccharide


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 483.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: acarbose-derived trisaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1722 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#11: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#12: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#13: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1652 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.7 % / Description: Thin parallelogram plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 1.5 M magnesium sulfate, 0.1 M MES buffer

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→200 Å / Num. obs: 245688 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 24.93 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.253 / Net I/σ(I): 33.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 6 / Num. unique obs: 24344 / Χ2: 1.439 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X7O

5x7o


Resolution: 1.95→152.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.391 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20779 11854 5 %RANDOM
Rwork0.17832 ---
obs0.17981 224154 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.004 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2---3.76 Å20 Å2
3---2.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.141 Å
Refinement stepCycle: 1 / Resolution: 1.95→152.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19202 0 596 1652 21450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0220280
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217264
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.95627719
X-RAY DIFFRACTIONr_angle_other_deg0.903340179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48352492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04424.163956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.132152798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.85215112
X-RAY DIFFRACTIONr_chiral_restr0.0780.23007
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024284
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_it1.5513.2349974
X-RAY DIFFRACTIONr_mcbond_other1.553.2349973
X-RAY DIFFRACTIONr_mcangle_it2.2754.84212464
X-RAY DIFFRACTIONr_mcangle_other2.2754.84312465
X-RAY DIFFRACTIONr_scbond_it1.973.4810306
X-RAY DIFFRACTIONr_scbond_other1.9683.4810306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9885.15615256
X-RAY DIFFRACTIONr_long_range_B_refined4.59238.47122991
X-RAY DIFFRACTIONr_long_range_B_other4.55138.33222840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 942 -
Rwork0.249 16796 -
obs--99.31 %

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