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- PDB-9u7v: The X-ray Crystallographic Structure of oligo-1,6-glucosidase fro... -

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Basic information

Entry
Database: PDB / ID: 9u7v
TitleThe X-ray Crystallographic Structure of oligo-1,6-glucosidase from Paenibacillus sp. STB16
Componentsoligo-1,6-glucosidase
KeywordsHYDROLASE / oligo-1 / 6-glucosidase / Mesophilic amylase / Isomaltooligosaccharide debranching enzyme
Function / homology
Function and homology information


oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / alpha-amylase activity / oligosaccharide catabolic process / cytoplasm
Similarity search - Function
: / Alpha-amylase SusG C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
oligo-1,6-glucosidase
Similarity search - Component
Biological speciesPaenibacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsLi, Z.F. / Tian, Y.X. / Zhang, J.S. / Ban, X.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32472281 China
CitationJournal: To Be Published
Title: The X-ray Crystallographic Structure of oligo-1,6-glucosidase from Paenibacillus sp. STB16
Authors: Li, Z.F. / Tian, Y.X. / Zhang, J.S. / Ban, X.F.
History
DepositionMar 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oligo-1,6-glucosidase
B: oligo-1,6-glucosidase


Theoretical massNumber of molelcules
Total (without water)134,2482
Polymers134,2482
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.570, 154.570, 115.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein oligo-1,6-glucosidase


Mass: 67123.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus (bacteria) / Gene: malL, BN871_GC_00040 / Production host: Bacillus subtilis (bacteria) / References: UniProt: W8YZE1, oligo-1,6-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8
Details: 0.2M Ammonium acetate, 0.1M Tris pH 8.0, 16% PEG 10000
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.24→31.44 Å / Num. obs: 19869 / % possible obs: 88.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 4.4
Reflection shellResolution: 3.24→3.5 Å / Rmerge(I) obs: 0.191 / Num. unique obs: 83744

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→31.44 Å / Cor.coef. Fo:Fc: 0.774 / Cor.coef. Fo:Fc free: 0.69 / SU B: 49.263 / SU ML: 0.785 / Cross valid method: THROUGHOUT / ESU R Free: 0.837 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34966 1016 5.1 %RANDOM
Rwork0.30487 ---
obs0.30715 18768 86.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.457 Å2
Baniso -1Baniso -2Baniso -3
1--5.89 Å2-0 Å2-0 Å2
2---5.89 Å2-0 Å2
3---11.78 Å2
Refinement stepCycle: 1 / Resolution: 3.24→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8929 0 0 65 8994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0129163
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168255
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.82712396
X-RAY DIFFRACTIONr_angle_other_deg0.3761.78418965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45251083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.704584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.181101517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022326
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_it1.174.5384353
X-RAY DIFFRACTIONr_mcbond_other1.174.5384353
X-RAY DIFFRACTIONr_mcangle_it2.0938.1585429
X-RAY DIFFRACTIONr_mcangle_other2.0938.1595430
X-RAY DIFFRACTIONr_scbond_it0.9084.5494810
X-RAY DIFFRACTIONr_scbond_other0.9084.554811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6798.3526968
X-RAY DIFFRACTIONr_long_range_B_refined4.17641.8210713
X-RAY DIFFRACTIONr_long_range_B_other4.17641.8210709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.24→3.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 75 -
Rwork0.39 1383 -
obs--89.23 %

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