Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.27 kDa 
• Atom Count: 3164 
• Modelled Residue Count: 160 
• Deposited Residue Count: 160 
• Unique protein chains: 1

4KJL

Room Temperature N23PPS148A DHFR

• PDB DOI: 10.2210/pdb4KJL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-03 Released: 2013-08-21 
• Deposition Author(s): van den Bedem, H., Bhabha, G., Yang, K., Wright, P.E., Fraser, J.S.

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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 

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

• PubMed: 23913260 
• 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. 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.

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Organizational Affiliation: 

Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford, California, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	160	Escherichia coli K-12	Mutation(s): 2  Gene Names: folA, UTI89_C0054, tmrA, b0048, JW0047 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4  Go to UniProtKB:  P0ABQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
FOL	B [auth A]	FOLIC ACID C19 H19 N7 O6 OVBPIULPVIDEAO-LBPRGKRZSA-N

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 = 34.64	α = 90
b = 45.76	β = 90
c = 98.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
ELVES	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-03 
• Released Date: 2013-08-21 
Deposition Author(s): van den Bedem, H., Bhabha, G., Yang, K., Wright, P.E., Fraser, J.S.

Revision History  

• 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