3VCC | pdb_00003vcc

CRYSTAL STRUCTURE OF D-Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg

• PDB DOI: https://doi.org/10.2210/pdb3VCC/pdb

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


• Deposited: 2012-01-03 Released: 2013-01-09 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF D-Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg

Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.05 kDa 
• Atom Count: 6,726 
• Modeled Residue Count: 771 
• Deposited Residue Count: 784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B	392	Paenibacillus sp. Y412MC10	Mutation(s): 0  Gene Names: GYMC10_3367

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.347	α = 90
b = 65.985	β = 93.56
c = 75.636	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description