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- PDB-3vgf: Crystal structure of glycosyltrehalose trehalohydrolase (D252S) c... -

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Basic information

Entry
Database: PDB / ID: 3vgf
TitleCrystal structure of glycosyltrehalose trehalohydrolase (D252S) 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
alpha-maltotriose / CITRATE ANION / Malto-oligosyltrehalose trehalohydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)65,9609
Polymers64,7141
Non-polymers1,2468
Water4,540252
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)131,92018
Polymers129,4272
Non-polymers2,49216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8000 Å2
ΔGint7 kcal/mol
Surface area40450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.441, 78.441, 282.277
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: 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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
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: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 23, 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: 2.3→94.09 Å / Num. obs: 45920 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 40.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.5 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å67.93 Å
Translation2.6 Å67.93 Å

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Processing

Software
NameVersionClassificationNB
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: 2.3→68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1977 / WRfactor Rwork: 0.1608 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8489 / SU B: 10.961 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1877 / SU Rfree: 0.1708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 2314 5 %RANDOM
Rwork0.1774 ---
obs0.1794 45823 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.51 Å2 / Biso mean: 47.1878 Å2 / Biso min: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å21.46 Å20 Å2
2--2.92 Å20 Å2
3----4.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 83 252 4887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224750
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9686412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30924.426244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.68715812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.751523
X-RAY DIFFRACTIONr_chiral_restr0.1530.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213632
X-RAY DIFFRACTIONr_mcbond_it0.7921.52756
X-RAY DIFFRACTIONr_mcangle_it1.52124457
X-RAY DIFFRACTIONr_scbond_it2.55631994
X-RAY DIFFRACTIONr_scangle_it3.9994.51955
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 168 -
Rwork0.236 3092 -
all-3260 -
obs--98.94 %
Refinement TLS params.Method: refined / Origin x: 11.5591 Å / Origin y: 33.4307 Å / Origin z: 22.4017 Å
111213212223313233
T0.0174 Å20.052 Å20.0042 Å2-0.2331 Å20.0136 Å2--0.0051 Å2
L0.5368 °20.0106 °20.2761 °2-0.2168 °2-0.074 °2--1.3193 °2
S0.0474 Å °-0.0353 Å °0.0096 Å °0.0012 Å °-0.0108 Å °0.0026 Å °-0.0071 Å °-0.1771 Å °-0.0365 Å °

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