[English] 日本語
Yorodumi
- PDB-8eym: CRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM SHEWANEL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eym
TitleCRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM SHEWANELLA DENITRIFICANS OS217 IN COMPLEX WITH GLUCITOLAMINE-6-PHOSPHATE AND N-ACETYLGLUCOSAMINE-6-PHOSPHATE AT 2.31 A RESOLUTION
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsISOMERASE / GLUCOSAMINE-6_PHOSPHATE DEAMINASE ISOMERASE SHEWANELLA DENITRIFICANS
Function / homology
Function and homology information


carbohydrate derivative metabolic process / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / carbohydrate derivative binding / cytoplasm
Similarity search - Function
GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily
Similarity search - Domain/homology
Chem-16G / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE / Glutamine-fructose-6-phosphate transaminase (Isomerizing)
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.311 Å
AuthorsRodriguez-Hernandez, A. / Marcos-Viquez, J. / Rodriguez-Romero, A. / Bustos-Jaimes, I.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)315896 Mexico
CitationJournal: Protein Sci. / Year: 2023
Title: Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS-fold glucosamine-6-phosphate deaminases.
Authors: Marcos-Viquez, J. / Rodriguez-Hernandez, A. / Alvarez-Anorve, L.I. / Medina-Garcia, A. / Plumbridge, J. / Calcagno, M.L. / Rodriguez-Romero, A. / Bustos-Jaimes, I.
History
DepositionOct 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0796
Polymers70,9542
Non-polymers1,1254
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-41 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.181, 80.237, 91.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Mass: 35476.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: No density was observed for the first two residues (MET & THR) and the last 12 residues due to disorder.
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): 469008 / References: UniProt: Q12KP2
#2: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-AGP / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE


Mass: 261.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16NO8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.25 M Tris-HCl pH 8.5, 30% w/v PEG 4000. Crystals containing GlcNol6P and GlcNAc6P grew in the presence of 1 mM GlcNAc6P and were soaked in the crystallization drop with 1 mM ...Details: 0.2 M MgCl2, 0.25 M Tris-HCl pH 8.5, 30% w/v PEG 4000. Crystals containing GlcNol6P and GlcNAc6P grew in the presence of 1 mM GlcNAc6P and were soaked in the crystallization drop with 1 mM GlcNol6P five minutes before freezing for data collection.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.31→39.75 Å / Num. obs: 22873 / % possible obs: 94.41 % / Redundancy: 4.6 % / CC1/2: 0.945 / Net I/σ(I): 36.1
Reflection shellResolution: 2.31→2.35 Å / Rmerge(I) obs: 0.223 / Num. unique obs: 2757

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SdNagBII-GlcNol6P

Resolution: 2.311→39.746 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 998 4.36 %
Rwork0.1856 --
obs0.1877 22873 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.311→39.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 70 177 4955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084857
X-RAY DIFFRACTIONf_angle_d1.0566629
X-RAY DIFFRACTIONf_dihedral_angle_d6.0133438
X-RAY DIFFRACTIONf_chiral_restr0.078831
X-RAY DIFFRACTIONf_plane_restr0.007839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.311-2.43250.35221250.24352757X-RAY DIFFRACTION85
2.4325-2.58490.2551350.23582933X-RAY DIFFRACTION90
2.5849-2.78440.28831390.23633048X-RAY DIFFRACTION93
2.7844-3.06460.25351410.2223135X-RAY DIFFRACTION96
3.0646-3.50780.26311490.19413236X-RAY DIFFRACTION98
3.5078-4.41850.19631510.15463303X-RAY DIFFRACTION99
4.4185-390.2031580.15973463X-RAY DIFFRACTION99

+
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://pdbjlvh1.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