[English] 日本語
Yorodumi
- PDB-6ldq: Sucrose-phosphate synthase (tll1590)_27_220_406_426_from Thermosy... -

+
Open data


ID or keywords:

Loading...

-
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 / nucleotide binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris

-
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

-
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

+
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