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- PDB-3hje: Crystal structure of sulfolobus tokodaii hypothetical maltooligos... -

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Basic information

Entry
Database: PDB / ID: 3hje
TitleCrystal structure of sulfolobus tokodaii hypothetical maltooligosyl trehalose synthase
Components704aa long hypothetical glycosyltransferase
KeywordsTRANSFERASE / trehalose biosynthesis / maltooligoside trehalose synthase (MTSase) / family 13 glycoside hydrolases / Sulfolobus tokodaii / tyrosine cluster
Function / homology
Function and homology information


(1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase / (1,4)-alpha-D-glucan 1-alpha-D-glucosylmutase 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
Maltooligosyltrehalose synthase
Similarity search - Component
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCielo, C.B.C. / Okazaki, S. / Suzuki, A. / Mizushima, T. / Masui, R. / Kuramitsu, S. / Yamane, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of ST0929, a putative glycosyl transferase from Sulfolobus tokodaii
Authors: Cielo, C.B.C. / Okazaki, S. / Suzuki, A. / Mizushima, T. / Masui, R. / Kuramitsu, S. / Yamane, T.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 704aa long hypothetical glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0985
Polymers83,7301
Non-polymers3684
Water15,457858
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.992, 86.100, 70.130
Angle α, β, γ (deg.)90.00, 95.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 704aa long hypothetical glycosyltransferase / Hypothetical maltooligosyl trehalose synthase


Mass: 83729.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: strain 7 / Gene: ST0929 / Plasmid: PET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: Q973H2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.89
Details: 0.2M Potassium sodium tartrate tetrahydrate, 20%(w/v) PEG3350, pH 5.89, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 11, 2007
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→69.843 Å / Num. obs: 59664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IV8

1iv8


Resolution: 1.9→19.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.08 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The flagged residues in REMARK 500 all fit very well within the observed electron densities. ASP 49, PHE 188, THR 393 are found in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The flagged residues in REMARK 500 all fit very well within the observed electron densities. ASP 49, PHE 188, THR 393 are found in approximately the same position as in corresponding residues observed in the molecular replacement search model, 1IV8 (Sulfolobus acidocaldarius Maltooligosyl trehalose synthase). On the other hand, the remaining residues do not match residues in the molecular replacement search model although, except for LYS 635, the corresponding residues in the molecular replacement search model are located in the proximity of these residues albeit in a different conformation.
RfactorNum. reflection% reflectionSelection details
Rfree0.20606 3014 5.1 %RANDOM
Rwork0.17065 ---
obs0.17245 56580 --
all-59664 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.399 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5902 0 24 858 6784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226213
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9638394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61324.316329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.702151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5281540
X-RAY DIFFRACTIONr_chiral_restr0.080.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024722
X-RAY DIFFRACTIONr_nbd_refined0.1820.23110
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2774
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.233
X-RAY DIFFRACTIONr_mcbond_it0.5421.53719
X-RAY DIFFRACTIONr_mcangle_it0.925860
X-RAY DIFFRACTIONr_scbond_it1.41332856
X-RAY DIFFRACTIONr_scangle_it2.1574.52523
LS refinement shellResolution: 1.897→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 228 -
Rwork0.252 4056 -
obs--96.81 %

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