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- PDB-9u5l: 4-alpha-glucanotransferase from Thermus thermophilus STB20 -

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Basic information

Entry
Database: PDB / ID: 9u5l
Title4-alpha-glucanotransferase from Thermus thermophilus STB20
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / Alpha amylase / Thermoduric / Disproportionation
Function / homologyGlycoside hydrolase, family 77 / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / cytoplasm / 4-alpha-glucanotransferase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, Z.F. / Tian, Y.X. / Xiao, Y. / 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 4-alpha-glycosyltransferase from Thermus thermophilus STB20
Authors: Li, Z.F. / Tian, Y.X. / Xiao, Y. / Ban, X.F.
History
DepositionMar 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)57,3991
Polymers57,3991
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.783, 41.391, 58.458
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 4-alpha-glucanotransferase / Amylomaltase / Disproportionating enzyme / D-enzyme


Mass: 57399.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: malQ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O87172, 4-alpha-glucanotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, 35% PEG 3350 / PH range: 5.5-6.5

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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: 2.1→40.5 Å / Num. obs: 27285 / % possible obs: 98.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→8.91 Å / Num. unique obs: 27285 / Rrim(I) all: 0.136

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.5 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.822 / SU B: 7.612 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31558 1333 4.9 %RANDOM
Rwork0.26431 ---
obs0.26675 25946 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-29.91 Å20 Å20.6 Å2
2---7.07 Å2-0 Å2
3----22.84 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 0 149 4182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163860
X-RAY DIFFRACTIONr_angle_refined_deg0.961.8385718
X-RAY DIFFRACTIONr_angle_other_deg0.3631.7528872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.874539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05410643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
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_it0.8172.5031997
X-RAY DIFFRACTIONr_mcbond_other0.8172.5031997
X-RAY DIFFRACTIONr_mcangle_it1.3944.52498
X-RAY DIFFRACTIONr_mcangle_other1.3934.52499
X-RAY DIFFRACTIONr_scbond_it0.6772.5882203
X-RAY DIFFRACTIONr_scbond_other0.6772.5882204
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1874.7163221
X-RAY DIFFRACTIONr_long_range_B_refined2.70924.944836
X-RAY DIFFRACTIONr_long_range_B_other2.69624.84830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 93 -
Rwork0.267 1824 -
obs--94.9 %

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