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- PDB-2x6r: Crystal structure of trehalose synthase TreT from P.horikoshi pro... -

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Basic information

Entry
Database: PDB / ID: 2x6r
TitleCrystal structure of trehalose synthase TreT from P.horikoshi produced by soaking in trehalose
ComponentsTREHALOSE-SYNTHASE TRET
KeywordsISOMERASE
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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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
Water7,098394
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)80.852, 63.067, 92.492
Angle α, β, γ (deg.)90.00, 98.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TREHALOSE-SYNTHASE TRET


Mass: 48237.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / 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.: 394 / 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: 2.42 Å3/Da / Density % sol: 45.41 % / 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→29.81 Å / Num. obs: 42278 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 6 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 11.4 / % possible all: 85

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XA1

2xa1


Resolution: 2.2→29.81 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 124998.23 / 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
Rfree0.26 2111 5 %RANDOM
Rwork0.224 ---
obs0.224 42278 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.7654 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.2 Å2
2---2.59 Å20 Å2
3---3.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6721 0 0 394 7115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.951.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it3.072
X-RAY DIFFRACTIONc_scangle_it4.462.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 323 5.2 %
Rwork0.253 5892 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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