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- PDB-2r60: Structure of apo Sucrose Phosphate Synthase (SPS) of Halothermoth... -

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Basic information

Entry
Database: PDB / ID: 2r60
TitleStructure of apo Sucrose Phosphate Synthase (SPS) of Halothermothrix orenii
ComponentsGlycosyl transferase, group 1
KeywordsTRANSFERASE / Rossmann-fold
Function / homology
Function and homology information


sucrose-phosphate synthase / sucrose-phosphate synthase activity
Similarity search - Function
Sucrose-phosphate synthase / Sucrose synthase / Sucrose synthase first GT-B domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose-phosphate synthase / :
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSivaraman, J. / Chua, T.K.
CitationJournal: Plant Cell / Year: 2008
Title: The Structure of Sucrose Phosphate Synthase from Halothermothrix orenii Reveals Its Mechanism of Action and Binding Mode.
Authors: Chua, T.K. / Bujnicki, J.M. / Tan, T.C. / Huynh, F. / Patel, B.K. / Sivaraman, J.
History
DepositionSep 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl transferase, group 1


Theoretical massNumber of molelcules
Total (without water)56,8831
Polymers56,8831
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.225, 48.499, 75.051
Angle α, β, γ (deg.)90.00, 100.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycosyl transferase, group 1


Mass: 56882.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Gene: SPS / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2ADF5, UniProt: B2CCB8*PLUS, sucrose-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Sequence details(MET A 1), (VAL A 2), (GLU A 3) ARE PART OF THE GENE PRODUCT

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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: 49.23 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 49698 / % possible obs: 97.2 % / Redundancy: 6.7 % / Net I/σ(I): 12.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.1 % / Num. unique all: 3851 / % possible all: 75.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 1.8→20 Å / σ(F): 6152
RfactorNum. reflection% reflection
Rfree0.252 4056 8 %
Rwork0.226 --
obs-40405 79.5 %
Solvent computationBsol: 69.321 Å2
Displacement parametersBiso mean: 35.322 Å2
Baniso -1Baniso -2Baniso -3
1-9.722 Å20 Å2-0.899 Å2
2---5.373 Å20 Å2
3----4.349 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 0 345 3956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.404
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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