9EOL | pdb_00009eol

N-acetylglucosamine 6-phosphate dehydratase: inhibited 6-phosphogluconic acid state of NagS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

A new pathway in central metabolism mediates nutrient control of development and antibiotic production by Streptomyces

Li, C., Urem, M., Kotsogianni, I., Lau, J., Elsayed, S.S., Martin, N.I., McNae, I.W., Voskamp, P., Mayer, C., Rigali, S., Pannu, N., Abrahams, J.P., Schada von Borzyskowski, L., van Wezel, G.P.

(2024) bioRxiv 


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0309 protein SCO4393
A, B
251Streptomyces coelicolorMutation(s): 0 
Gene Names: SCO4393, SCD10.25c
UniProt
Find proteins for Q9K3V1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9K3V1 
Go to UniProtKB:  Q9K3V1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K3V1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.668α = 90
b = 87.668β = 90
c = 278.81γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Scholarship CouncilChina201904910552
Netherlands Organisation for Scientific Research (NWO)Netherlands10379

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release