[English] 日本語
Yorodumi
- PDB-3s28: The crystal structure of sucrose synthase-1 in complex with a bre... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Non-polymers , 5 types, 490 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
#5: Chemical...
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more