3QL3 | pdb_00003ql3

Re-refined coordinates for PDB entry 1RX2

• PDB DOI: https://doi.org/10.2210/pdb3QL3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-02 Released: 2011-04-27 
• Deposition Author(s): Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1RX2

Literature

A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

Bhabha, G., Lee, J., Ekiert, D.C., Gam, J., Wilson, I.A., Dyson, H.J., Benkovic, S.J., Wright, P.E.

(2011) Science 332: 234-238

• PubMed: 21474759 
• DOI: https://doi.org/10.1126/science.1198542
• Primary Citation of Related Structures:  
  3QL0, 3QL3


• PubMed Abstract: 
  

  Conformational dynamics play a key role in enzyme catalysis. Although protein motions have clear implications for ligand flux, a role for dynamics in the chemical step of enzyme catalysis has not been clearly established. We generated a mutant of Escherichia coli dihydrofolate reductase that abrogates millisecond-time-scale fluctuations in the enzyme active site without perturbing its structural and electrostatic preorganization. This dynamic knockout severely impairs hydride transfer. Thus, we have found a link between conformational fluctuations on the millisecond time scale and the chemical step of an enzymatic reaction, with broad implications for our understanding of enzyme mechanisms and for design of novel protein catalysts.

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Organizational Affiliation: 

Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 19.32 kDa 
• Atom Count: 1,481 
• Modelled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	159	Escherichia coli K-12	Mutation(s): 0  Gene Names: folA, 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 3 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
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.32	α = 90
b = 45.51	β = 90
c = 98.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Other
• Version 1.3: 2011-09-28
  Changes: Other
• Version 1.4: 2012-04-25
  Changes: Other
• Version 1.5: 2014-11-12
  Changes: Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references, Derived calculations