3P3B | pdb_00003p3b

CRYSTAL STRUCTURE OF Galacturonate DEHYDRATASE FROM GEOBACILLUS SP. COMPLEXED WITH D-TARTRATE

• PDB DOI: https://doi.org/10.2210/pdb3P3B/pdb

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


• Deposited: 2010-10-04 Released: 2011-06-29 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

CRYSTAL STRUCTURE OF Galacturonate DEHYDRATASE FROM GEOBACILLUS SP. COMPLEXED WITH D-TARTRATE.

Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Burley, S.K., 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: 88.24 kDa 
• Atom Count: 6,208 
• Modeled Residue Count: 741 
• 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
TAR	E [auth A], H [auth B]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-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: 1.65 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.859	α = 90
b = 66.051	β = 95.48
c = 75.664	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: 2011-06-29 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-14
  Changes: Database references, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references