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- PDB-1eha: CRYSTAL STRUCTURE OF GLYCOSYLTREHALOSE TREHALOHYDROLASE FROM SULF... -

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Basic information

Entry
Database: PDB / ID: 1eha
TitleCRYSTAL STRUCTURE OF GLYCOSYLTREHALOSE TREHALOHYDROLASE FROM SULFOLOBUS SOLFATARICUS
ComponentsGLYCOSYLTREHALOSE TREHALOHYDROLASE
KeywordsHYDROLASE / trehalose / trehalohydrolase / Sulfolobus solfataricus / alpha-beta barrel / calcium binding / covalent dimer
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
Malto-oligosyltrehalose trehalohydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / Isomorphous Replacement / Resolution: 3 Å
AuthorsFeese, M.D. / Kato, Y. / Tamada, T. / Kato, M. / Komeda, T. / Kobayashi, K. / Kuroki, R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus.
Authors: Feese, M.D. / Kato, Y. / Tamada, T. / Kato, M. / Komeda, T. / Miura, Y. / Hirose, M. / Hondo, K. / Kobayashi, K. / Kuroki, R.
History
DepositionFeb 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 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: GLYCOSYLTREHALOSE TREHALOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)64,7381
Polymers64,7381
Non-polymers00
Water54030
1
A: GLYCOSYLTREHALOSE TREHALOHYDROLASE

A: GLYCOSYLTREHALOSE TREHALOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)129,4752
Polymers129,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)80.366, 80.366, 281.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GLYCOSYLTREHALOSE TREHALOHYDROLASE / TREHALOHYDROLASE / GTHASE


Mass: 64737.723 Da / Num. of mol.: 1 / Mutation: C298V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PUCBG1 / Production host: Pichia jadinii (fungus) / References: UniProt: Q55088, alpha-amylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.1 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6-1.1 M sodium citrate 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
20.6-1.1 Msodium citrate1drop
30.1 MHEPES1drop

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Data collection

DiffractionMean temperature: 282 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: CHARLES SUPPER DOUBLE-MIRROR FOCUSING SYSTEM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→55.9 Å / Num. all: 93107 / Num. obs: 21534 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.6
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.4 / % possible all: 73
Reflection
*PLUS
% possible obs: 93 % / Observed criterion σ(F): 2 / Num. measured all: 93107
Reflection shell
*PLUS
% possible obs: 73 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TNT5Erefinement
RefinementMethod to determine structure: Isomorphous Replacement
Starting model: 1EH9

1eh9


Resolution: 3→20 Å / Stereochemistry target values: Engh & Huber / Details: Conjugate direction
Num. reflection% reflectionSelection details
all21490 --
obs20393 93 %-
Rfree--CCP4 Uniqueify script
Solvent computationSolvent model: Moews and Kretsinger (1975) J. Mol. Biol., 91:201-228
Bsol: 608.444 Å2 / ksol: 0.914 e/Å3
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 0 30 4572
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01546611.15
X-RAY DIFFRACTIONt_angle_deg2.3662883
X-RAY DIFFRACTIONt_dihedral_angle_d23.35727220
X-RAY DIFFRACTIONt_trig_c_planes0.0141311.75
X-RAY DIFFRACTIONt_gen_planes0.0146707.7
X-RAY DIFFRACTIONt_nbd0.0233030
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Num. reflection Rfree: 1097 / % reflection Rfree: 5 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_planar_d0.0251.75
X-RAY DIFFRACTIONt_plane_restr0.0147.7
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Rfactor Rfree: 0.404 / Rfactor obs: 0.276

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