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- PDB-3s28: The crystal structure of sucrose synthase-1 in complex with a bre... -

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Basic information

Entry
Database: PDB / ID: 3s28
TitleThe crystal structure of sucrose synthase-1 in complex with a breakdown product of the UDP-glucose
ComponentsSucrose synthase 1
KeywordsTRANSFERASE / Glycosyltransferase / Sucrose metabolism / sugar donar complex / Rossmann fold / GT-B fold / Glycosyltansferase / UDP-glucose / cytosol
Function / homology
Function and homology information


sucrose synthase / response to flooding / sucrose synthase activity / response to mannitol / response to sorbitol / sucrose metabolic process / response to sucrose / response to water deprivation / plasmodesma / response to osmotic stress ...sucrose synthase / response to flooding / sucrose synthase activity / response to mannitol / response to sorbitol / sucrose metabolic process / response to sucrose / response to water deprivation / plasmodesma / response to osmotic stress / response to glucose / response to cold / cellular response to hypoxia / response to hypoxia / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1230 / Nuclear Transport Factor 2; Chain: A, - #330 / Sucrose synthase, plant/cyanobacteria / Sucrose synthase / Sucrose synthase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Nuclear Transport Factor 2; Chain: A, / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1230 / Nuclear Transport Factor 2; Chain: A, - #330 / Sucrose synthase, plant/cyanobacteria / Sucrose synthase / Sucrose synthase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Nuclear Transport Factor 2; Chain: A, / Four Helix Bundle (Hemerythrin (Met), subunit A) / Roll / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 1,5-anhydro-D-arabino-hex-1-enitol / MALONIC ACID / 1,5-anhydro-D-fructose / URIDINE-5'-DIPHOSPHATE / Sucrose synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZheng, Y. / Garavito, R.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications.
Authors: Zheng, Y. / Anderson, S. / Zhang, Y. / Garavito, R.M.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 2.0Apr 22, 2020Group: Atomic model / Database references / Category: atom_site / struct_ref_seq_dif
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_atom_id / _atom_site.label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Jul 29, 2020Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn ...pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Sucrose synthase 1
B: Sucrose synthase 1
C: Sucrose synthase 1
D: Sucrose synthase 1
E: Sucrose synthase 1
F: Sucrose synthase 1
G: Sucrose synthase 1
H: Sucrose synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)762,70772
Polymers753,4298
Non-polymers9,27864
Water7,963442
1
A: Sucrose synthase 1
B: Sucrose synthase 1
C: Sucrose synthase 1
D: Sucrose synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,35436
Polymers376,7144
Non-polymers4,63932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-241 kcal/mol
Surface area115560 Å2
MethodPISA
2
E: Sucrose synthase 1
F: Sucrose synthase 1
G: Sucrose synthase 1
H: Sucrose synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,35436
Polymers376,7144
Non-polymers4,63932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-243 kcal/mol
Surface area114800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.750, 261.880, 160.190
Angle α, β, γ (deg.)90.00, 108.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Sucrose synthase 1 / / Sucrose-UDP glucosyltransferase 1


Mass: 94178.617 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: col / Gene: At5g20830, SUS1, T1M15.230 / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3) / References: UniProt: P49040, sucrose synthase

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Sugars , 2 types, 16 molecules

#3: Sugar
ChemComp-LCN / 1,5-anhydro-D-arabino-hex-1-enitol


Type: D-saccharide / Mass: 162.141 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H10O5
#4: Sugar
ChemComp-NHF / 1,5-anhydro-D-fructose


Type: D-saccharide / Mass: 162.141 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H10O5

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Non-polymers , 5 types, 490 molecules

#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 1.85-1.90 M AMMONIUM SULFATE, 80-100 MM SODIUM CITRATE pH 6.1, 0.15 M SODIUM POTASSIUM TARTRATE, 150 mM SUCROSE, 5 mM URIDINE DIPHOSPHATE GLUCOSE, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2010
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.8→185.269 Å / Num. all: 263585 / Num. obs: 263585 / % possible obs: 99.7 % / Redundancy: 3 % / Rsym value: 0.114 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.8-2.9530.6151.3385270.615100
2.95-3.1330.382364890.38100
3.13-3.3530.2383.2342520.238100
3.35-3.6130.1455.3318920.14599.9
3.96-36.6130.0997.5293380.09999.9
3.96-4.4330.07210265310.07299.7
4.43-5.1130.0611.6233620.0699.6
5.11-6.2630.06211.2197180.06299.5
6.26-8.8530.04413.5152260.04499.1
8.85-50.0582.90.03513.382500.03597.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S27

3s27


Resolution: 2.8→24.976 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8349 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 13244 5.03 %
Rwork0.1879 --
obs0.1903 263089 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.04 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 174.61 Å2 / Biso mean: 47.6281 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.1171 Å20 Å20.3638 Å2
2--0.5596 Å20 Å2
3----0.4425 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50122 0 560 442 51124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151867
X-RAY DIFFRACTIONf_angle_d1.13970339
X-RAY DIFFRACTIONf_chiral_restr0.0847696
X-RAY DIFFRACTIONf_plane_restr0.0068989
X-RAY DIFFRACTIONf_dihedral_angle_d15.53119207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.83180.35774200.303830487248304100
2.8318-2.8650.33264460.286836088068360100
2.865-2.89990.3244610.2849831387748313100
2.8999-2.93660.32784290.2833834887778348100
2.9366-2.97520.31154450.2603838488298384100
2.9752-3.01590.32424780.265825887368258100
3.0159-3.05890.29264090.2518835287618352100
3.0589-3.10440.31434460.2484832887748328100
3.1044-3.15290.3144430.2374834187848341100
3.1529-3.20450.27435020.2233833788398337100
3.2045-3.25960.2684650.219830287678302100
3.2596-3.31870.27673890.2137838187708381100
3.3187-3.38240.24524480.2011829987478299100
3.3824-3.45130.24054620.1867834788098347100
3.4513-3.52610.23254420.1878838188238381100
3.5261-3.60790.23644510.1797825787088257100
3.6079-3.69790.23794250.1718838888138388100
3.6979-3.79750.22114300.1707834987798349100
3.7975-3.90890.21744290.1648835787868357100
3.9089-4.03450.19964390.1556832087598320100
4.0345-4.17810.18974470.1458833087778330100
4.1781-4.34450.20614680.1492832987978329100
4.3445-4.54110.17964280.1421833787658337100
4.5411-4.7790.17934140.1421834787618347100
4.779-5.07610.20184700.151582738743827399
5.0761-5.46420.23434170.1749841088278410100
5.4642-6.00710.22664020.186183348736833499
6.0071-6.86060.23294430.180283218764832199
6.8606-8.58490.1924430.157283308773833099
8.5849-24.97720.20894530.184481288581812896

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