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- PDB-3vge: Crystal structure of glycosyltrehalose trehalohydrolase (D252S) -

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Basic information

Entry
Database: PDB / ID: 3vge
TitleCrystal structure of glycosyltrehalose trehalohydrolase (D252S)
ComponentsMalto-oligosyltrehalose trehalohydrolase4-alpha-D-((1-4)-alpha-D-glucano)trehalose trehalohydrolase
KeywordsHYDROLASE / alpha/beta barrel / trehalose / trehalohydrolase / alpha-amylase
Function / homology
Function and homology information


4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase / 4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity / trehalose biosynthetic process / cytoplasm
Similarity search - Function
Malto-oligosyltrehalose trehalohydrolase, archaeal, C-terminal / Alpha-amylase, C terminal / Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / Malto-oligosyltrehalose trehalohydrolase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Malto-oligosyltrehalose trehalohydrolase, archaeal, C-terminal / Alpha-amylase, C terminal / Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / Malto-oligosyltrehalose trehalohydrolase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Malto-oligosyltrehalose trehalohydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsOkazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2012
Title: Substrate recognition mechanism of a glycosyltrehalose trehalohydrolase from Sulfolobus solfataricus KM1.
Authors: Okazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Blaber, M. / Kuroki, R.
History
DepositionAug 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5479
Polymers64,7141
Non-polymers8348
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules

A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,09518
Polymers129,4272
Non-polymers1,66816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5730 Å2
ΔGint-13 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.506, 78.506, 282.444
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2111-

HOH

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Components

#1: Protein Malto-oligosyltrehalose trehalohydrolase / 4-alpha-D-((1-4)-alpha-D-glucano)trehalose trehalohydrolase / MTHase / 4-alpha-D-((1->4)-alpha-D-glucano)trehalose trehalohydrolase / Glycosyltrehalose ...MTHase / 4-alpha-D-((1->4)-alpha-D-glucano)trehalose trehalohydrolase / Glycosyltrehalose trehalohydrolase / GTHase / Maltooligosyl trehalose trehalohydrolase


Mass: 64713.723 Da / Num. of mol.: 1 / Mutation: D252S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: treZ / Plasmid: PGUSS2 / Production host: Pichia jadinii (fungus)
References: UniProt: Q55088, 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1M sodium citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2002 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→94.15 Å / Num. obs: 27427 / Redundancy: 6.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 18.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 2.9 / % possible all: 89.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å61.26 Å
Translation3 Å61.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EH9

1eh9


Resolution: 2.7→61.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1861 / WRfactor Rwork: 0.1427 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8866 / SU B: 18.997 / SU ML: 0.175 / SU R Cruickshank DPI: 0.3852 / SU Rfree: 0.2653 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.21188 1384 5 %RANDOM
Rwork0.15914 ---
obs0.16177 26037 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.23 Å2 / Biso mean: 40.901 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å21.55 Å20 Å2
2--3.1 Å20 Å2
3----4.66 Å2
Refinement stepCycle: LAST / Resolution: 2.7→61.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 55 165 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9616364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4375554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3724.426244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.2915812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9051523
X-RAY DIFFRACTIONr_chiral_restr0.140.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213632
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_it0.8461.52756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68324457
X-RAY DIFFRACTIONr_scbond_it2.71931963
X-RAY DIFFRACTIONr_scangle_it4.5464.51907
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 106 -
Rwork0.219 1704 -
all-1810 -
obs--88.42 %
Refinement TLS params.Method: refined / Origin x: 11.6172 Å / Origin y: 33.4469 Å / Origin z: 22.4289 Å
111213212223313233
T0.0083 Å20.0243 Å20.0032 Å2-0.1086 Å20.0109 Å2--0.0381 Å2
L0.3205 °20.0134 °20.1424 °2-0.0243 °20.0019 °2--0.6792 °2
S0.0243 Å °-0.0036 Å °-0.0039 Å °0.0035 Å °-0.0057 Å °-0.012 Å °-0.0115 Å °-0.0816 Å °-0.0186 Å °

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