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- PDB-2x6q: Crystal structure of trehalose synthase TreT from P.horikoshi -

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Basic information

Entry
Database: PDB / ID: 2x6q
TitleCrystal structure of trehalose synthase TreT from P.horikoshi
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
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSong, H.-N. / Jung, T.-Y. / Yoon, S.-M. / Lim, M.-Y. / Lee, S.-B. / 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
DepositionFeb 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TREHALOSE-SYNTHASE TRET
B: TREHALOSE-SYNTHASE TRET


Theoretical massNumber of molelcules
Total (without water)96,4752
Polymers96,4752
Non-polymers00
Water4,900272
1
A: TREHALOSE-SYNTHASE TRET


Theoretical massNumber of molelcules
Total (without water)48,2381
Polymers48,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TREHALOSE-SYNTHASE TRET


Theoretical massNumber of molelcules
Total (without water)48,2381
Polymers48,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.788, 63.655, 90.651
Angle α, β, γ (deg.)90.00, 99.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999803, -0.010977, 0.01653), (0.010702, -0.999804, -0.016686), (0.01671, -0.016506, 0.999724)
Vector: 90.07294, 47.26453, -0.46063)

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Components

#1: Protein TREHALOSE-SYNTHASE TRET / PUTATIVE UNCHARACTERIZED PROTEIN PH1035


Mass: 48237.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Plasmid: P6XHIS119 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 / References: UniProt: O58762
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.34 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growDetails: PEG 3350 25%, 0.2M MGCL2, 0.1M SODIUM HEPES BUFFER

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399
DetectorDate: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.2→29.99 Å / Num. obs: 41687 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.95 / % possible all: 80.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 335657.3 / 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
Rfree0.258 2077 5 %RANDOM
Rwork0.227 ---
obs0.227 41687 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0601 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å23.95 Å2
2---2.97 Å20 Å2
3---1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 0 272 6983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.611.5
X-RAY DIFFRACTIONc_mcangle_it4.692
X-RAY DIFFRACTIONc_scbond_it5.672
X-RAY DIFFRACTIONc_scangle_it7.582.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 2.2 Å / Weight position: 29.99
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.489 216 5 %
Rwork0.482 4096 -
obs--56.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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