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- PDB-2r66: Complex Structure of Sucrose Phosphate Synthase (SPS)-F6P of Halo... -

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Basic information

Entry
Database: PDB / ID: 2r66
TitleComplex Structure of Sucrose Phosphate Synthase (SPS)-F6P of Halothermothrix orenii
ComponentsGlycosyl transferase, group 1Glycosyltransferase
KeywordsTRANSFERASE / Rossmann-fold
Function / homology
Function and homology information


sucrose-phosphate synthase / sucrose-phosphate synthase activity / sucrose synthase activity / sucrose metabolic process
Similarity search - Function
Sucrose synthase / Sucrose synthase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / sucrose-phosphate synthase / :
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1432
Polymers56,8831
Non-polymers2601
Water2,126118
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.)90.000, 100.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycosyl transferase, group 1 / Glycosyltransferase / Sucrose Phosphate Synthase


Mass: 56882.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: SPS / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2ADF5, UniProt: B8CZ51*PLUS, sucrose-phosphate synthase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose / Fructose 6-phosphate


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST THREE RESIDUES, MET 1, VAL 2, AND GLU 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 0.6M NaCl, 0.1M Na MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13734 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Χ2: 1.394 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.93.60.28213481.321100
2.9-3.023.60.22813861.366100
3.02-3.153.70.18513321.468100
3.15-3.323.70.14513641.503100
3.32-3.533.70.10613701.515100
3.53-3.83.70.08713671.564100
3.8-4.183.70.06413751.445100
4.18-4.793.70.05413851.412100
4.79-6.033.70.05113921.244100
6.03-503.50.03314151.09798.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R60

2r60


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1282 8.4 %RANDOM
Rwork0.21 ---
obs-12600 82.8 %-
Solvent computationBsol: 52.904 Å2
Displacement parametersBiso mean: 46.807 Å2
Baniso -1Baniso -2Baniso -3
1-12.226 Å20 Å2-8.539 Å2
2---1.764 Å20 Å2
3----10.462 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 16 118 3745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.062
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3f6p.param

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