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- PDB-9isa: Dimeric amylosucrase from Deinococcus geothermalis -

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Basic information

Entry
Database: PDB / ID: 9isa
TitleDimeric amylosucrase from Deinococcus geothermalis
ComponentsAmylosucrase
KeywordsCARBOHYDRATE / amylosucrase / dimerization / sucrose isomer
Function / homology
Function and homology information


amylosucrase activity / carbohydrate metabolic process
Similarity search - Function
: / Amylosucrase, C-terminal domain / Amylosucrase, catalytic 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
Biological speciesDeinococcus geothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKim, D.S. / Park, J.H. / Seo, D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1C1C1004489 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Construction and enzymatic characterization of a monomeric variant of dimeric amylosucrase from Deinococcus geothermalis.
Authors: Oh, J.S. / Kim, D.S. / So, Y.S. / Hong, S. / Yoo, S.H. / Park, C.S. / Park, J.H. / Seo, D.H.
History
DepositionJul 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 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: Amylosucrase
B: Amylosucrase


Theoretical massNumber of molelcules
Total (without water)145,6102
Polymers145,6102
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-6 kcal/mol
Surface area46850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.917, 149.917, 188.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRAA7 - 6462 - 641
2LEULEUBB6 - 6461 - 641

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Components

#1: Protein Amylosucrase


Mass: 72805.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis (strain DSM 11300 / CIP 105573 / AG-3a) (bacteria)
Gene: Dgeo_0572
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: Q1J0W0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.69→48.3 Å / Num. obs: 49477 / % possible obs: 87.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.8
Reflection shellResolution: 2.69→2.84 Å / Rmerge(I) obs: 0.458 / Num. unique obs: 7656

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UER

3uer


Resolution: 2.69→46.22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.461 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21985 2544 4.9 %RANDOM
Rwork0.17642 ---
obs0.17855 49477 86.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.843 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å2-0 Å20 Å2
2--1.16 Å20 Å2
3----2.33 Å2
Refinement stepCycle: 1 / Resolution: 2.69→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10119 0 0 40 10159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.63314143
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85151264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22619.73667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28151620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.41515129
X-RAY DIFFRACTIONr_chiral_restr0.1260.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028208
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.7464.7175071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.2217.066330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4565.1545330
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.76661.29614598
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 20564 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.693→2.763 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 186 -
Rwork0.327 3666 -
obs--88.55 %

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