4N15

Crystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, with bound beta-D-glucuronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRAP dicarboxylate transporter, DctP subunit335Burkholderia ambifaria AMMDMutation(s): 0 
Gene Names: Bamb_6123
UniProt
Find proteins for Q0B2F6 (Burkholderia ambifaria (strain ATCC BAA-244 / AMMD))
Explore Q0B2F6 
Go to UniProtKB:  Q0B2F6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0B2F6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDP
Query on BDP

Download Ideal Coordinates CCD File 
C [auth A]beta-D-glucopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.19α = 90
b = 101.781β = 90
c = 55.522γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-3000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary