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- PDB-3vgh: Crystal structure of glycosyltrehalose trehalohydrolase (E283Q) c... -

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Basic information

Entry
Database: PDB / ID: 3vgh
TitleCrystal structure of glycosyltrehalose trehalohydrolase (E283Q) complexed with maltotriosyltrehalose
ComponentsMalto-oligosyltrehalose 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 / Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / 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 / Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / 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 / Resolution: 2.6 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0356
Polymers64,7411
Non-polymers1,2945
Water2,936163
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)132,07012
Polymers129,4822
Non-polymers2,58810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8080 Å2
ΔGint37 kcal/mol
Surface area40770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.801, 78.801, 282.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Malto-oligosyltrehalose 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: 64740.754 Da / Num. of mol.: 1 / Mutation: E283Q
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: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-1DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a1-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-FLC / CITRATE ANION


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


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


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1M sodium citrate, 0.1M HEPES, 5mM MTT, 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: Jan 24, 2001 / 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: 2.6→55.3 Å / Num. obs: 31666 / % possible obs: 97.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.7 / % possible all: 81.7

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Processing

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

1eh9


Resolution: 2.6→55.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8372 / SU B: 20.066 / SU ML: 0.192 / SU R Cruickshank DPI: 0.3451 / SU Rfree: 0.2605 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1600 5.1 %RANDOM
Rwork0.1941 ---
obs0.1966 31605 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.31 Å2 / Biso mean: 45.7887 Å2 / Biso min: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 87 163 4799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224756
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9716426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24624.449245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15615812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3741523
X-RAY DIFFRACTIONr_chiral_restr0.0830.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213632
X-RAY DIFFRACTIONr_mcbond_it0.3251.52751
X-RAY DIFFRACTIONr_mcangle_it0.63524450
X-RAY DIFFRACTIONr_scbond_it0.83932005
X-RAY DIFFRACTIONr_scangle_it1.4814.51976
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 93 -
Rwork0.3 1690 -
all-1783 -
obs--76.39 %
Refinement TLS params.Method: refined / Origin x: 11.7367 Å / Origin y: 33.686 Å / Origin z: 22.5008 Å
111213212223313233
T0.0179 Å20.0475 Å20.009 Å2-0.1712 Å20.0151 Å2--0.1329 Å2
L0.8892 °20.1198 °20.3078 °2-0.3967 °2-0.067 °2--1.8866 °2
S0.0286 Å °-0.0324 Å °0.0243 Å °-0.0055 Å °0.0064 Å °0.0251 Å °0.0064 Å °-0.2434 Å °-0.035 Å °

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