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- PDB-3s29: The crystal structure of sucrose synthase-1 from Arabidopsis thal... -

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Basic information

Entry
Database: PDB / ID: 3s29
TitleThe crystal structure of sucrose synthase-1 from Arabidopsis thaliana and its functional implications.
ComponentsSucrose synthase 1
KeywordsTRANSFERASE / Glycosyltransferase / Sucrose metabolism / sugar acceptor complex / Rossmann Fold / GT-B fold / UDP / Fructose / cytosol
Function / homology
Function and homology information


sucrose synthase / sucrose synthase activity / response to flooding / response to mannitol / response to sorbitol / sucrose metabolic process / response to sucrose / response to water deprivation / plasmodesma / response to osmotic stress ...sucrose synthase / sucrose synthase activity / response to flooding / 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
: / : / Sucrose synthase N-terminal / Sucrose synthase EPBD domain / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1230 / Nuclear Transport Factor 2; Chain: A, - #330 / Sucrose synthase, plant/cyanobacteria / Sucrose synthase / Sucrose synthase first GT-B domain / Glycosyl transferase, family 1 ...: / : / Sucrose synthase N-terminal / Sucrose synthase EPBD domain / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1230 / Nuclear Transport Factor 2; Chain: A, - #330 / Sucrose synthase, plant/cyanobacteria / Sucrose synthase / Sucrose synthase first GT-B domain / 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
beta-D-fructofuranose / : / MALONIC ACID / URIDINE-5'-DIPHOSPHATE / Sucrose synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZheng, Y.I. / 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 1.1Sep 14, 2011Group: Other
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 13, 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: 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)762,54774
Polymers753,4298
Non-polymers9,11866
Water8,989499
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)381,16936
Polymers376,7144
Non-polymers4,45532
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18550 Å2
ΔGint-263 kcal/mol
Surface area115870 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)381,37838
Polymers376,7144
Non-polymers4,66334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19090 Å2
ΔGint-273 kcal/mol
Surface area115220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)277.160, 261.500, 161.100
Angle α, β, γ (deg.)90.00, 109.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 16 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
#3: Sugar
ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 557 molecules

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


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


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 499 / 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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.85-1.90 M AMMONIUM SULFATE, 80-100 MM SODIUM CITRATE pH 5.8, 0.15 M SODIUM POTASSIUM TARTRATE, 20 mM FRUCTOSE, 5 mM URIDINE DIPHOSPHATE, 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: 2.85→49.596 Å / Num. all: 249743 / Num. obs: 249743 / % possible obs: 99.4 % / Redundancy: 2.6 % / Rsym value: 0.135 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.85-32.60.6811.194390364680.68199.5
3-3.192.60.4391.789113344940.43999.6
3.19-3.412.60.2862.583599324340.28699.5
3.41-3.682.60.177477499301680.17799.5
3.68-4.032.60.125.971257278250.1299.6
4.03-4.512.60.0848.664433251550.08499.7
4.51-5.22.60.06710.757017221950.06799.5
5.2-6.372.60.06810.748441187640.06899.6
6.37-9.012.60.04414.937158144460.04498.9
9.01-49.5962.50.02521.81916577940.02597.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S27

3s27


Resolution: 2.85→24.964 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8443 / SU ML: 0.38 / σ(F): 0 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 11886 4.77 %
Rwork0.1846 --
obs0.1869 249276 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.056 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 148.86 Å2 / Biso mean: 46.1547 Å2 / Biso min: 15.47 Å2
Baniso -1Baniso -2Baniso -3
1--2.032 Å20 Å23.3724 Å2
2--5.0575 Å20 Å2
3----3.0255 Å2
Refinement stepCycle: LAST / Resolution: 2.85→24.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50443 0 538 499 51480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152156
X-RAY DIFFRACTIONf_angle_d1.07970715
X-RAY DIFFRACTIONf_chiral_restr0.087734
X-RAY DIFFRACTIONf_plane_restr0.0059041
X-RAY DIFFRACTIONf_dihedral_angle_d15.73219389
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 (%)
2.85-2.88230.35483940.303279148308791499
2.8823-2.91620.3523970.3004788182787881100
2.9162-2.95170.30833910.272678668257786699
2.9517-2.9890.32784000.277279408340794099
2.989-3.02820.33533950.2741791983147919100
3.0282-3.06970.30493980.257794283407942100
3.0697-3.11340.31343980.2533791683147916100
3.1134-3.15980.32243940.24278808274788099
3.1598-3.20910.3153950.2393788082757880100
3.2091-3.26160.28393980.2248793683347936100
3.2616-3.31770.28573920.227785082427850100
3.3177-3.37790.25733990.211379578356795799
3.3779-3.44270.25653940.197179128306791299
3.4427-3.51280.24523960.187979328328793299
3.5128-3.5890.23273960.1831790483007904100
3.589-3.67220.24923980.188479168314791699
3.6722-3.76370.22413970.1731792983267929100
3.7637-3.86510.21063970.1598790282997902100
3.8651-3.97840.21173970.159795083477950100
3.9784-4.10630.20273970.1512790883057908100
4.1063-4.25240.19813950.1452794683417946100
4.2524-4.42170.18583970.1386793783347937100
4.4217-4.62180.16643970.130779478344794799
4.6218-4.86380.2043950.143279168311791699
4.8638-5.1660.19613990.150479048303790499
5.166-5.56080.22583990.1733796983687969100
5.5608-6.11290.23853970.178879318328793199
6.1129-6.98050.20993980.171679578355795799
6.9805-8.73170.18143950.150579188313791898
8.7317-24.9650.183910.166577318122773196

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