[English] 日本語
Yorodumi
- PDB-5jqq: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jqq
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / UDP-alpha-D-glucose metabolic process / hexosyltransferase activity / magnesium ion binding / protein homodimerization activity
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAlbesa-Jove, D. / Urresti, S. / Gest, P.M. / van der Woerd, M. / Jackson, M. / Guerin, M.E.
CitationJournal: To Be Published
Title: Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form
Authors: Albesa-Jove, D. / Romero-Garcia, J. / Sancho-Vaello, E. / Contreras, F.-X. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Biarnes, X. / Planas, A. / Guerin, M.E.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Revision 1.2Dec 10, 2025Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7673
Polymers36,5831
Non-polymers1842
Water1,06359
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5346
Polymers73,1652
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4010 Å2
ΔGint-25 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.850, 98.850, 127.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

-
Components

#1: Protein Glucosyl-3-phosphoglycerate synthase


Mass: 36582.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: gpgS, Rv1208 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 mM MgCl2, 100 mM sodium cacodylate pH 6.5, 200 mM trisodium citrate, 30%(v/v) 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 22, 2008
Details: Rosenbaum-Rock Si(111) sagitally focused monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→41.77 Å / Num. obs: 37009 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.106 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CKJ

1ckj


Resolution: 2.6→39.077 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 26.54
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1904 5.14 %Random selection
Rwork0.2089 ---
obs0.2101 37009 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 12 59 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072224
X-RAY DIFFRACTIONf_angle_d1.1533037
X-RAY DIFFRACTIONf_dihedral_angle_d13.115810
X-RAY DIFFRACTIONf_chiral_restr0.047364
X-RAY DIFFRACTIONf_plane_restr0.007390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.66520.35111290.33712408X-RAY DIFFRACTION100
2.6652-2.73730.38581580.33122522X-RAY DIFFRACTION100
2.7373-2.81780.34261040.26872513X-RAY DIFFRACTION100
2.8178-2.90870.24491350.25422582X-RAY DIFFRACTION100
2.9087-3.01260.25131200.24722513X-RAY DIFFRACTION100
3.0126-3.13320.28081510.23842512X-RAY DIFFRACTION100
3.1332-3.27570.2581120.24122485X-RAY DIFFRACTION100
3.2757-3.44830.34681500.24122511X-RAY DIFFRACTION100
3.4483-3.66420.23891510.19532517X-RAY DIFFRACTION100
3.6642-3.94690.21631670.2022502X-RAY DIFFRACTION100
3.9469-4.34360.19941400.17962492X-RAY DIFFRACTION100
4.3436-4.97110.18011400.15772518X-RAY DIFFRACTION100
4.9711-6.25890.22371380.19822505X-RAY DIFFRACTION100
6.2589-39.08120.1761090.1852525X-RAY DIFFRACTION100

+
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