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- PDB-5x7s: Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltra... -

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Basic information

Entry
Database: PDB / ID: 5x7s
TitleCrystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase, terbium derivative
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) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / : / Glycosyl hydrolase family 31 C-terminal domain ...: / : / Domain of unknown function DUF5110 / Carbohydrate binding module (family 35) / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / TERBIUM(III) ION / Glycoside hydrolase family 31 alpha-glucosidase
Similarity search - Component
Biological speciesPaenibacillus sp. 598K (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id

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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)279,66550
Polymers275,3682
Non-polymers4,29748
Water20,3571130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34220 Å2
ΔGint-401 kcal/mol
Surface area80820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.815, 270.920, 133.341
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-2488-

HOH

21B-2568-

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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Non-polymers , 8 types, 1178 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Tb
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1130 / 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: 3.04 Å3/Da / Density % sol: 59.51 % / 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, 1 mM terbium chloride

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.64883,1.64955,1.60679
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.648831
21.649551
31.606791
ReflectionResolution: 2.4→200 Å / Num. obs: 128840 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.115 / Χ2: 2.045 / Net I/σ(I): 29.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6364 / Χ2: 1.109 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→151.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.743 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.255 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23871 5912 5 %RANDOM
Rwork0.18458 ---
obs0.18727 113142 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.741 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å20 Å20 Å2
2---5.64 Å20 Å2
3---2.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.376 Å
Refinement stepCycle: 1 / Resolution: 2.4→151.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19202 0 173 1130 20505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0219862
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216938
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.93327129
X-RAY DIFFRACTIONr_angle_other_deg0.995339317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26552494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28524.169957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.224152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.52515112
X-RAY DIFFRACTIONr_chiral_restr0.0950.22870
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02122829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024279
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_it3.2264.6079976
X-RAY DIFFRACTIONr_mcbond_other3.2254.6069975
X-RAY DIFFRACTIONr_mcangle_it4.4286.90112467
X-RAY DIFFRACTIONr_mcangle_other4.4276.90112468
X-RAY DIFFRACTIONr_scbond_it3.5964.789886
X-RAY DIFFRACTIONr_scbond_other3.5964.789886
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9867.08614662
X-RAY DIFFRACTIONr_long_range_B_refined6.41353.22522571
X-RAY DIFFRACTIONr_long_range_B_other6.39353.1822484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 441 -
Rwork0.285 8575 -
obs--95.75 %

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