[English] 日本語
Yorodumi
- PDB-9gre: Cryo-electron microscopy structure of glucose/xylose isomerase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gre
TitleCryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with magnesium ions in the active site
ComponentsXylose isomerase
KeywordsMETAL BINDING PROTEIN / magnesium / isomerase / sugars / glucose / xylose / metal ion / Cryo-EM
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsSlawek, J. / Klonecka, A. / Rawski, M. / Kozak, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/39/O/ST4/03465 Poland
CitationJournal: To Be Published
Title: Cryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with magnesium ions in the active site
Authors: Slawek, J. / Klonecka, A. / Rawski, M. / Kozak, M.
History
DepositionSep 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
C: Xylose isomerase
D: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,32812
Polymers173,1334
Non-polymers1948
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and (resid 2 through 204 or resid 206 through 388 or resid 401 through 402))
d_2ens_1(chain "A" and (resid 2 through 204 or resid 206 through 388 or resid 401 through 402))
d_3ens_1(chain "C" and (resid 2 through 204 or resid 206 through 388 or resid 401 through 402))
d_4ens_1(chain "D" and (resid 2 through 204 or resid 206 through 388 or resid 401 through 402))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNGLUGLUBB2 - 2042 - 204
d_12LEULEUGLYGLYBB206 - 388206 - 388
d_13MGMGMGMGBG401
d_21ASNASNGLUGLUAA2 - 2042 - 204
d_22LEULEUGLYGLYAA206 - 388206 - 388
d_23MGMGMGMGAE401
d_31ASNASNGLUGLUCC2 - 2042 - 204
d_32LEULEUGLYGLYCC206 - 388206 - 388
d_33MGMGMGMGCI401
d_41ASNASNGLUGLUDD2 - 2042 - 204
d_42LEULEUGLYGLYDD206 - 388206 - 388
d_43MGMGMGMGDK401

NCS oper:
IDCodeMatrixVector
1given(-0.99999995898065, 0.00026038557766057, -0.00011932332887036), (-0.00026040806658138, -0.99999994832888, 0.00018849368073903), (-0.00011927424166885, 0.00018852474576452, 0.99999997511604)215.02742813885, 215.04863093431, -0.0004813371482868
2given(-0.99999999367416, -6.0035989399599E-5, 9.5117595824634E-5), (-6.0031554266741E-5, 0.99999999711093, 4.6630059571782E-5), (-9.5120395031594E-5, 4.6624349219692E-5, -0.99999999438914)215.03729544525, 0.0061255528910635, 213.36430782469
3given(0.99999999652008, 4.0393544833417E-5, -7.2994565514978E-5), (4.0391385146786E-5, -0.99999999874654, -2.9588182943386E-5), (-7.2995760595077E-5, 2.9585234488812E-5, -0.99999999689817)0.0076702291865303, 215.02909811777, 213.3632601645

-
Components

#1: Protein
Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / Plasmid details: Hampton Research / References: UniProt: P24300, xylose isomerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: glucose/xylose isomerase with cobalt ions / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.043 MDa / Experimental value: NO
Source (natural)Organism: Streptomyces rubiginosus (bacteria)
Buffer solutionpH: 7.4 / Details: 50 mM PBS pH 7.4
Buffer componentConc.: 50 mM / Name: Phosphate-buffered saline / Formula: PBS
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6038653
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1284479 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008512520
ELECTRON MICROSCOPYf_angle_d0.822416952
ELECTRON MICROSCOPYf_chiral_restr0.05761744
ELECTRON MICROSCOPYf_plane_restr0.01052312
ELECTRON MICROSCOPYf_dihedral_angle_d4.79351736
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints3.446703558813E-13
ens_1d_3BBELECTRON MICROSCOPYNCS constraints1.4025407307563E-12
ens_1d_4BBELECTRON MICROSCOPYNCS constraints8.8249037924685E-13

+
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