3P0W | pdb_00003p0w

Crystal structure of D-Glucarate dehydratase from Ralstonia solanacearum complexed with Mg and D-glucarate

• PDB DOI: https://doi.org/10.2210/pdb3P0W/pdb

• Classification: ISOMERASE
• Organism(s): Ralstonia pickettii 12J
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-29 Released: 2010-10-13 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., 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: 1.71 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Crystal structure of D-Glucarate dehydratase from Ralstonia solanacearum complexed with Mg and D-glucarate

Fedorov, A.A., Fedorov, E.V., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 205.64 kDa 
• Atom Count: 13,261 
• Modeled Residue Count: 1,698 
• Deposited Residue Count: 1,880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D	470	Ralstonia pickettii 12J	Mutation(s): 0  Gene Names: Rpic_4449 EC: 4.2.1.40
UniProt
Find proteins for B2UIZ1 (Ralstonia pickettii (strain 12J)) Explore B2UIZ1  Go to UniProtKB:  B2UIZ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKR	F [auth A], H [auth B], J [auth C], L [auth D]	D-GLUCARATE C6 H8 O8 DSLZVSRJTYRBFB-LLEIAEIESA-L
MG	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.958	α = 90
b = 128.822	β = 90
c = 178.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Gerlt, J.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references