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- PDB-3s27: The crystal structure of sucrose synthase-1 from Arabidopsis thal... -

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Basic information

Entry
Database: PDB / ID: 3s27
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 / 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
beta-D-fructofuranose / : / MALONIC ACID / URIDINE-5'-DIPHOSPHATE / Sucrose synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.91 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 1.3Jul 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.pdbx_leaving_atom_flag / _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

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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)766,80764
Polymers758,6818
Non-polymers8,12556
Water10,142563
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)383,40332
Polymers379,3414
Non-polymers4,06328
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17590 Å2
ΔGint-227 kcal/mol
Surface area116510 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)383,40332
Polymers379,3414
Non-polymers4,06328
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17300 Å2
ΔGint-227 kcal/mol
Surface area115910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.212, 263.704, 159.663
Angle α, β, γ (deg.)90.00, 108.80, 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: 94835.180 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): B843 (DE3) / References: UniProt: P49040, sucrose synthase
#3: Sugar
ChemComp-FRU / beta-D-fructofuranose


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, 611 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.: 24 / 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.: 8 / 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.: 563 / 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: 3.63 Å3/Da / Density % sol: 66.14 %
Crystal growTemperature: 293 K / 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, 2 mM DITHIOTHREITOL, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9794
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2010
RadiationMonochromator: Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 232828 / % possible obs: 99.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.719 / % possible all: 89.7

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.76 / FOM acentric: 0.76 / FOM centric: 0.66 / Reflection: 191382 / Reflection acentric: 188411 / Reflection centric: 2971
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.1-3.30.570.570.483478334439344
3.3-3.90.730.730.685741956771648
3.9-4.40.830.830.743259432133461
4.4-5.50.850.850.713246331911552
5.5-8.90.830.840.662587025277593
8.9-500.850.860.682537880373

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.15phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.91→25 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 0 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 10738 5 %
Rwork0.186 --
obs0.189 214680 91 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 36.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.4139 Å20 Å23.7914 Å2
2--3.4514 Å2-0 Å2
3----0.0374 Å2
Refinement stepCycle: LAST / Resolution: 2.91→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50240 0 480 563 51283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151900
X-RAY DIFFRACTIONf_angle_d1.13670405
X-RAY DIFFRACTIONf_dihedral_angle_d16.38419216
X-RAY DIFFRACTIONf_chiral_restr0.087710
X-RAY DIFFRACTIONf_plane_restr0.0059002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.908-2.94050.35991820.34393823X-RAY DIFFRACTION51
2.9405-2.97510.43212620.32435175X-RAY DIFFRACTION70
2.9751-3.01130.34562540.31785660X-RAY DIFFRACTION75
3.0113-3.04930.39273170.29665933X-RAY DIFFRACTION80
3.0493-3.08940.34433100.27996157X-RAY DIFFRACTION82
3.0894-3.13160.31063400.2546439X-RAY DIFFRACTION86
3.1316-3.17630.29293500.24586413X-RAY DIFFRACTION86
3.1763-3.22360.28323590.23026497X-RAY DIFFRACTION88
3.2236-3.27390.29943630.21986627X-RAY DIFFRACTION89
3.2739-3.32740.25943340.21056758X-RAY DIFFRACTION90
3.3274-3.38470.26763610.2026811X-RAY DIFFRACTION92
3.3847-3.44610.23753720.18716905X-RAY DIFFRACTION93
3.4461-3.51220.25013770.1797015X-RAY DIFFRACTION94
3.5122-3.58360.23713830.18337023X-RAY DIFFRACTION94
3.5836-3.66130.2283620.17127074X-RAY DIFFRACTION95
3.6613-3.74620.23083530.1587171X-RAY DIFFRACTION95
3.7462-3.83960.20393960.1567164X-RAY DIFFRACTION96
3.8396-3.9430.20573690.15297201X-RAY DIFFRACTION96
3.943-4.05860.20883860.14447284X-RAY DIFFRACTION97
4.0586-4.1890.19333720.13957264X-RAY DIFFRACTION97
4.189-4.3380.18573780.14167326X-RAY DIFFRACTION98
4.338-4.51070.1873970.13647320X-RAY DIFFRACTION99
4.5107-4.71470.1754100.13667338X-RAY DIFFRACTION98
4.7147-4.96140.19133780.14037343X-RAY DIFFRACTION98
4.9614-5.26950.21613920.1727359X-RAY DIFFRACTION98
5.2695-5.6720.22383900.18377347X-RAY DIFFRACTION98
5.672-6.23480.24273920.18517343X-RAY DIFFRACTION98
6.2348-7.11870.22214150.1897389X-RAY DIFFRACTION98
7.1187-8.9010.22014090.17737452X-RAY DIFFRACTION99
8.901-24.99720.25163750.21997331X-RAY DIFFRACTION96

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