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- PDB-1iv8: Crystal Structure of Maltooligosyl trehalose synthase -

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Basic information

Entry
Database: PDB / ID: 1iv8
TitleCrystal Structure of Maltooligosyl trehalose synthase
ComponentsMALTOOLIGOSYL TREHALOSE SYNTHASE
KeywordsISOMERASE / TREHALOSE SYNTHASE / BETA ALPHA BARREL / INTRAMOLECULAR TRANSGLUCOSYLATION
Function / homology
Function and homology information


catalytic activity / carbohydrate metabolic process
Similarity search - Function
Malto-oligosyltrehalose synthase, C-terminal / Domain of unknown function (DUF1953) / Maltooligosyl trehalose synthase; domain 4 / Maltooligosyl trehalose synthase; domain 3 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Malto-oligosyltrehalose synthase, C-terminal / Domain of unknown function (DUF1953) / Maltooligosyl trehalose synthase; domain 4 / Maltooligosyl trehalose synthase; domain 3 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / DNA polymerase; domain 1 / Glycosidases / Arc Repressor Mutant, subunit A / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycosyltrehalose-producing enzyme
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsKobayashi, M. / Kubota, M. / Matsuura, Y.
CitationJournal: J.APPL.Glyosci. / Year: 2003
Title: Refined Structure and Functional Implications of Trehalose Synthase from Sulfolobus acidocaldarius
Authors: Kobayashi, M. / Kubota, M. / Matsuura, Y.
History
DepositionMar 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTOOLIGOSYL TREHALOSE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)85,3111
Polymers85,3111
Non-polymers00
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.504, 68.497, 93.769
Angle α, β, γ (deg.)90.00, 101.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MALTOOLIGOSYL TREHALOSE SYNTHASE


Mass: 85310.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Plasmid: pKST9 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53688, (1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 2000, MAGNESIUM CHLORIDE, TRIS, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 60100 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 1.164 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 1.9→1.96 Å / % possible all: 89.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3667 8 %RANDOM
Rwork0.197 ---
obs-51748 --
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 0 366 6379

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