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- PDB-6ldq: Sucrose-phosphate synthase (tll1590)_27_220_406_426_from Thermosy... -

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Basic information

Entry
Database: PDB / ID: 6ldq
TitleSucrose-phosphate synthase (tll1590)_27_220_406_426_from Thermosynechococcus elongatus (twinned)
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 / THIOCYANATE ION / Tll1590 protein
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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
DepositionNov 22, 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: Tll1590 protein
A: Tll1590 protein
B: Tll1590 protein
C: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1388
Polymers99,9054
Non-polymers2324
Water4,035224
1
D: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0342
Polymers24,9761
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-5 kcal/mol
Surface area9550 Å2
MethodPISA
2
A: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0342
Polymers24,9761
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9630 Å2
MethodPISA
3
B: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0342
Polymers24,9761
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-5 kcal/mol
Surface area9400 Å2
MethodPISA
4
C: Tll1590 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0342
Polymers24,9761
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-5 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.022, 134.059, 60.794
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Tll1590 protein / Sucrose-phosphate synthase


Mass: 24976.361 Da / Num. of mol.: 4 / Mutation: 221-405 deletion
Source method: isolated from a genetically manipulated source
Details: deletion of residues 221-405 in Q8DIJ5
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Gene: tll1590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIJ5
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris

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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 PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.92→19.4 Å / Num. obs: 60298 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6.7
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.625 / Num. unique obs: 4059

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Processing

SoftwareName: PHENIX / Version: 1.16_3549 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KIH

6kih


Resolution: 1.92→19.398 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2908 2018 3.35 %
Rwork0.2405 58229 -
obs0.2422 60247 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.68 Å2 / Biso mean: 25.4208 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.92→19.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 12 224 6317
Biso mean--22.11 28.99 -
Num. residues----739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.9680.3351390.2762414499
1.968-2.02120.3461470.2704416299
2.0212-2.08060.3191410.2695411099
2.0806-2.14760.32911400.246409198
2.1476-2.22430.32321440.2484410698
2.2243-2.31320.33791480.246415599
2.3132-2.41830.30181450.2468414099
2.4183-2.54550.31731380.2418420299
2.5455-2.70460.31131420.23144140100
2.7046-2.91280.29531490.25234210100
2.9128-3.20480.32341410.2547416799
3.2048-3.66580.25371440.2248418699
3.6658-4.60830.26221480.2191420399
4.6083-19.3980.25541520.2385421399

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