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- PDB-6kih: Sucrose-phosphate synthase (tll1590) from Thermosynechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 6kih
TitleSucrose-phosphate synthase (tll1590) from Thermosynechococcus elongatus
ComponentsTll1590 protein
KeywordsTRANSFERASE / Sucrose-phosphate synthase
Function / homologyGlycosyl transferase 4-like domain / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / sucrose-6-phosphate / URIDINE-5'-DIPHOSPHATE / Tll1590 protein
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSu, J.
CitationJournal: Front Microbiol / Year: 2020
Title: Co-crystal Structure ofThermosynechococcus elongatusSucrose Phosphate Synthase With UDP and Sucrose-6-Phosphate Provides Insight Into Its Mechanism of Action Involving an Oxocarbenium Ion and the Glycosidic Bond.
Authors: Li, Y. / Yao, Y. / Yang, G. / Tang, J. / Ayala, G.J. / Li, X. / Zhang, W. / Han, Q. / Yang, T. / Wang, H. / Mayo, K.H. / Su, J.
History
DepositionJul 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Tll1590 protein
B: Tll1590 protein
C: Tll1590 protein
D: Tll1590 protein
E: Tll1590 protein
F: Tll1590 protein
G: Tll1590 protein
H: Tll1590 protein
I: Tll1590 protein
J: Tll1590 protein
K: Tll1590 protein
L: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)612,91533
Polymers604,26412
Non-polymers8,65021
Water00
1
A: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-6 kcal/mol
Surface area16320 Å2
MethodPISA
2
B: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7602
Polymers50,3551
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-9 kcal/mol
Surface area16180 Å2
MethodPISA
3
C: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-7 kcal/mol
Surface area16260 Å2
MethodPISA
4
D: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-8 kcal/mol
Surface area16190 Å2
MethodPISA
5
E: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area16320 Å2
MethodPISA
6
F: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area16140 Å2
MethodPISA
7
G: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7602
Polymers50,3551
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-8 kcal/mol
Surface area15950 Å2
MethodPISA
8
H: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area16270 Å2
MethodPISA
9
I: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area16350 Å2
MethodPISA
10
J: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7602
Polymers50,3551
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area16160 Å2
MethodPISA
11
K: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area16240 Å2
MethodPISA
12
L: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1823
Polymers50,3551
Non-polymers8262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-7 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.662, 170.835, 160.546
Angle α, β, γ (deg.)90.000, 96.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tll1590 protein / Sucrose-phosphate synthase


Mass: 50355.359 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Gene: tll1590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIJ5
#2: Polysaccharide
6-O-phosphono-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose-6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_6*OPO/3O/3=O][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}[(6+0)][P]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→19.9 Å / Num. obs: 122717 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.06 Å / Rmerge(I) obs: 0.855 / Num. unique obs: 5683

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Processing

SoftwareName: PHENIX / Version: 1.17_3644 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c4q

3c4q


Resolution: 3→19.9 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 2000 1.63 %
Rwork0.2661 120673 -
obs0.268 122673 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.12 Å2 / Biso mean: 80.6966 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37617 0 543 0 38160
Biso mean--77.06 --
Num. residues----4794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.080.35421370.32568247838495
3.08-3.160.32871430.287986498792100
3.16-3.260.35621430.2786688811100
3.26-3.360.32221440.258886368780100
3.36-3.480.3521430.244586838826100
3.48-3.620.35421440.228786708814100
3.62-3.780.27991450.213186958840100
3.78-3.980.30011430.213586528795100
3.98-4.230.29811430.200286438786100
4.23-4.550.24841420.17798584872699
4.55-50.23961430.16968648879199
5-5.710.24371440.18698681882599
5.71-7.140.27841420.20788565870798
7.14-19.90.21981440.1758652879698

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