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- PDB-2xa9: Crystal structure of trehalose synthase TreT mutant E326A from P.... -

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Basic information

Entry
Database: PDB / ID: 2xa9
TitleCrystal structure of trehalose synthase TreT mutant E326A from P. horikoshii in complex with UDPG
ComponentsTREHALOSE-SYNTHASE TRET
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


alpha,alpha-trehalose synthase / trehalose synthase activity / glucose metabolic process
Similarity search - Function
: / : / : / Trehalose synthase, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Trehalose synthase
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSong, H.-N. / Jung, T.-Y. / Yoon, S.-M. / Lee, S.-B. / Lim, M.-Y. / Woo, E.-J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Insights on the New Mechanism of Trehalose Synthesis by Trehalose Synthase Tret from Pyrococcus Horikoshii.
Authors: Woo, E.-J. / Ryu, S. / Song, H.-N. / Jung, T.-Y. / Yeon, S. / Lee, H. / Park, B.C. / Park, K. / Lee, S.-B.
History
DepositionMar 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TREHALOSE-SYNTHASE TRET
B: TREHALOSE-SYNTHASE TRET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4924
Polymers96,3592
Non-polymers1,1332
Water2,414134
1
A: TREHALOSE-SYNTHASE TRET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7462
Polymers48,1801
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TREHALOSE-SYNTHASE TRET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7462
Polymers48,1801
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.844, 63.139, 91.517
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TREHALOSE-SYNTHASE TRET / PH1035


Mass: 48179.516 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Description: HYPERTHERMOPHILIC ARCHAEON / Plasmid: P6XHIS119 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061(DE3) / References: UniProt: O58762
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 326 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 326 TO ALA

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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: 2.29 Å3/Da / Density % sol: 46.42 % / Description: NONE
Crystal growpH: 8.5
Details: PEG3350 25%, 0.2M MGCL2, 0.1M SODIUM HEPES BUFFER, 5MM UDPG, pH 8.5

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 30955 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→30 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.81 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 26725.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1534 5 %RANDOM
Rwork0.227 ---
obs0.227 30955 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5545 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å2-0.17 Å2
2---5.65 Å20 Å2
3---8.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 72 134 6954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.261.5
X-RAY DIFFRACTIONc_mcangle_it7.562
X-RAY DIFFRACTIONc_scbond_it7.662
X-RAY DIFFRACTIONc_scangle_it10.232.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 259 5.4 %
Rwork0.298 4515 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4UPG_XPLOR_PAR.TXTUPG_XPLOR_PAR.TXT

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