3CTP

Crystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with D-xylulofuranose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with L-xylulose.

Malashkevich, V.N.Toro, R.Wasserman, S.R.Meyer, A.Sauder, J.M.Burley, S.K.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic binding protein/LacI transcriptional regulator AB330Alkaliphilus metalliredigens QYMFMutation(s): 0 
Gene Names: Amet_0586
Find proteins for A6TKU5 (Alkaliphilus metalliredigens (strain QYMF))
Explore A6TKU5 
Go to UniProtKB:  A6TKU5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XLF
Query on XLF

Download Ideal Coordinates CCD File 
A, B
beta-D-xylulofuranose
C5 H10 O5
LQXVFWRQNMEDEE-MROZADKFSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.172α = 90
b = 61.903β = 104.81
c = 74.362γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-11-14
    Changes: Data collection, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2021-02-03
    Changes: Database references, Structure summary