4IP4 | pdb_00004ip4

Crystal structure of l-fuconate dehydratase from Silicibacter sp. tm1040 liganded with Mg

• PDB DOI: https://doi.org/10.2210/pdb4IP4/pdb

• Classification: ISOMERASE
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-09 Released: 2013-12-04 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Lukk, T., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of l-fuconate dehydratase from Silicibacter sp. tm1040 liganded with mg

Fedorov, A.A., Fedorov, E.V., Lukk, T., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 95.17 kDa 
• Atom Count: 7,167 
• Modeled Residue Count: 842 
• Deposited Residue Count: 850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme-like protein	A, B	425	Ruegeria sp. TM1040	Mutation(s): 0  Gene Names: TM1040_3391
UniProt
Find proteins for A0ACD6B8A2 (Ruegeria sp. (strain TM1040)) Explore A0ACD6B8A2  Go to UniProtKB:  A0ACD6B8A2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO2	F [auth A], G [auth A], J [auth B], K [auth B]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N
MG	E [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.051	α = 90
b = 141.332	β = 90
c = 59.778	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Lukk, T., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description