[English] 日本語
Yorodumi
- PDB-4de7: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4de7
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mg2+ and uridine-diphosphate (UDP)
ComponentsGLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / UDP-alpha-D-glucose metabolic process / hexosyltransferase activity / glycosyltransferase activity / magnesium ion binding / protein homodimerization activity / metal ion binding
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
URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAlbesa-Jove, D. / Urresti, S. / van der Woerd, M. / Guerin, M.E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria.
Authors: Urresti, S. / Albesa-Jove, D. / Schaeffer, F. / Pham, H.T. / Kaur, D. / Gest, P. / van der Woerd, M.J. / Carreras-Gonzalez, A. / Lopez-Fernandez, S. / Alzari, P.M. / Brennan, P.J. / Jackson, M. / Guerin, M.E.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1714
Polymers36,5831
Non-polymers5883
Water39622
1
A: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
hetero molecules

A: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3428
Polymers73,1652
Non-polymers1,1776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5130 Å2
ΔGint-20 kcal/mol
Surface area20920 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

#1: Protein GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)


Mass: 36582.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gpgS, MT1246, Rv1208 / Plasmid: pET28a-gpgS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 22 / 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: 4.26 Å3/Da / Density % sol: 71.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 mM MgCl2, 5mM UDP, 1.5M NaCl, 10%(v/v) ethanol, Tris-HCL pH 8.0, VAPOR DIFFUSION, SITTING 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
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→41.58 Å / Num. all: 12217 / Num. obs: 12217 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.22 % / Biso Wilson estimate: 68.5 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.08 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1205 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.077 Å / SU ML: 0.85 / σ(F): 1.46 / Phase error: 23.89 / Stereochemistry target values: ML
Details: AUTHORS STATE THE FOLLOWING ON THE DENSITY ON UDP. THE DENSITY IS VERY LOW, BUT WE DO BELIEVE THE LIGAND IS PRESENT. WE THINK THAT THE LOW OCCUPANCY AND THE PARTIAL DISORDER OF UDP MOLECULE ...Details: AUTHORS STATE THE FOLLOWING ON THE DENSITY ON UDP. THE DENSITY IS VERY LOW, BUT WE DO BELIEVE THE LIGAND IS PRESENT. WE THINK THAT THE LOW OCCUPANCY AND THE PARTIAL DISORDER OF UDP MOLECULE RESULTS IN VERY WEEK ELECTRON DENSITY. BOTH, THE ALPHA- AND BETA-PHOSPHATES OF UDP ARE DISORDERED, AND NO ELECTRON DENSITY IS VISIBLE FOR THEM. WE BELIEVE THE DISORDER OF PHOSPHATE GROUPS IS DUE TO THE ABSENCE OF DIVALENT CATION BOND TO THE STRUCTURE, WHICH USUALLY COORDINATES BETWEEN THE PHOSPHATE GROUPS AND THE ENZYME. COORDINATION OF THE DIVALENT CATION IS PH DEPENDENT, AT PH < 6 THE RESIDUE HIS258 IS FOUND PROTONATED, AND IS UNABLE TO COORDINATE DIVALENT CATIONS. WE BELIEVE THAT IS WHAT HAPPENS IN THIS CASE, RESULTING IN PARTIAL DISORDER OF UDP AND LOW OCCUPANCY. NONETHELESS, WEEK ELECTRON DENSITY IS FOUND FOR THE URIDINE MOIETY, SO WE FELL IT IS STILL INFORMATIVE TO INCLUDE IT IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 585 4.8 %RANDOM
Rwork0.2242 ---
obs0.2252 12193 98.43 %-
all-12387 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.265 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4203 Å20 Å2-0 Å2
2--2.4203 Å20 Å2
3----4.8407 Å2
Refinement stepCycle: LAST / Resolution: 3→39.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 28 22 2140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072196
X-RAY DIFFRACTIONf_angle_d0.9753013
X-RAY DIFFRACTIONf_dihedral_angle_d12.614807
X-RAY DIFFRACTIONf_chiral_restr0.057364
X-RAY DIFFRACTIONf_plane_restr0.009385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9941-3.29530.29931480.29942771X-RAY DIFFRACTION94
3.2953-3.77180.27281570.24182908X-RAY DIFFRACTION100
3.7718-4.75070.2361410.21582955X-RAY DIFFRACTION100
4.7507-39.08010.2151390.20092974X-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