3CSS

Crystal structure of 6-phosphogluconolactonase from Leishmania guyanensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.

Painter, J.Merritt, E.A.

(2006) Acta Crystallogr.,Sect.D 62: 439-450

  • DOI: 10.1107/S0907444906005270
  • Also Cited By: 3FOC, 2HQJ

  • PubMed Abstract: 
  • A single protein crystal structure contains information about dynamic properties of the protein as well as providing a static view of one three-dimensional conformation. This additional information is to be found in the distribution of observed elect ...

    A single protein crystal structure contains information about dynamic properties of the protein as well as providing a static view of one three-dimensional conformation. This additional information is to be found in the distribution of observed electron density about the mean position of each atom. It is general practice to account for this by refining a separate atomic displacement parameter (ADP) for each atomic center. However, these same displacements are often described well by simpler models based on TLS (translation/libration/screw) rigid-body motion of large groups of atoms, for example interdomain hinge motion. A procedure, TLSMD, has been developed that analyzes the distribution of ADPs in a previously refined protein crystal structure in order to generate optimal multi-group TLS descriptions of the constituent protein chains. TLSMD is applicable to crystal structures at any resolution. The models generated by TLSMD analysis can significantly improve the standard crystallographic residuals R and R(free) and can reveal intrinsic dynamic properties of the protein.


    Organizational Affiliation

    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphogluconolactonase
A
267Leishmania braziliensisMutation(s): 0 
EC: 3.1.1.31
Find proteins for A4HFB4 (Leishmania braziliensis)
Go to UniProtKB:  A4HFB4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 69.999α = 90.00
b = 89.381β = 90.00
c = 100.521γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
MAR345data collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description