4IM7 | pdb_00004im7

Crystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate

• PDB DOI: https://doi.org/10.2210/pdb4IM7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli CFT073
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-02 Released: 2013-01-23 
• Deposition Author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate

Wichelecki, S., Lukk, T., Imker, H.J., Nair, S.K., Gerlt, J.A.

To be published.

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: 56.89 kDa 
• Atom Count: 4,298 
• Modeled Residue Count: 483 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical oxidoreductase ydfI	A	506	Escherichia coli CFT073	Mutation(s): 0  Gene Names: c1968, ydfI EC: 1
UniProt
Find proteins for A0A0H2V7F2 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V7F2  Go to UniProtKB:  A0A0H2V7F2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
CS2	B [auth A]	D-MANNONIC ACID C6 H12 O7 RGHNJXZEOKUKBD-MBMOQRBOSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.49	α = 90
b = 92.49	β = 90
c = 136	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations