3QPE

Crystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate

• PDB DOI: https://doi.org/10.2210/pdb3QPE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Paenibacillus sp. Y412MC10
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-12 Released: 2012-02-15 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate

Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 176.7 kDa 
• Atom Count: 12,829 
• Modelled Residue Count: 1,517 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D	392	Paenibacillus sp. Y412MC10	Mutation(s): 0  Gene Names: GYMC10_3367
UniProt
Find proteins for D3EID5 (Geobacillus sp. (strain Y412MC10)) Explore D3EID5  Go to UniProtKB:  D3EID5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGU	G [auth A]	D-galacturonic acid C6 H10 O7 IAJILQKETJEXLJ-RSJOWCBRSA-N
D54	J [auth B], M [auth C], Q [auth D]	4-deoxy-L-threo-hex-5-ulosuronic acid C6 H8 O6 IMUGYKFHMJLTOU-UCORVYFPSA-N
GOL	N [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.019	α = 90
b = 66.265	β = 95.73
c = 154.609	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 2.0: 2020-07-01
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description