4KJL

Room Temperature N23PPS148A DHFR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Automated identification of functional dynamic contact networks from X-ray crystallography.

van den Bedem, H.Bhabha, G.Yang, K.Wright, P.E.Fraser, J.S.

(2013) Nat Methods 10: 896-902

  • DOI: 10.1038/nmeth.2592
  • Primary Citation of Related Structures:  
    4KJJ, 4KJK, 4KJL

  • PubMed Abstract: 
  • Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics ...

    Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics. Here we report a new algorithm, CONTACT, that identifies contact networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks determined for Escherichia coli dihydrofolate reductase (ecDHFR) predict the observed long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild-type and mutant ecDHFR suggests that mutations that alter optimized contact networks of coordinated motions can impair catalytic function. CONTACT-guided mutagenesis can exploit the structure-dynamics-function relationship in protein engineering and design.


    Organizational Affiliation

    Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford, California, USA. vdbedem@slac.stanford.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrofolate reductaseA160Escherichia coli K-12Mutation(s): 2 
Gene Names: folAUTI89_C0054tmrAb0048JW0047
EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Explore P0ABQ4 
Go to UniProtKB:  P0ABQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABQ4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
FOL
Query on FOL

Download Ideal Coordinates CCD File 
B [auth A]FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.64α = 90
b = 45.76β = 90
c = 98.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
ELVESrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description