3SQS | pdb_00003sqs

Crystal Structure of a putative mandelate racemase/muconate lactonizing protein from Dinoroseobacter shibae DFL 12

• PDB DOI: https://doi.org/10.2210/pdb3SQS/pdb

• Classification: ISOMERASE
• Organism(s): Dinoroseobacter shibae DFL 12 = DSM 16493
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-06 Released: 2011-07-27 
• Deposition Author(s): Kumaran, D., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a putative mandelate racemase/muconate lactonizing protein from Dinoroseobacter shibae DFL 12

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 46.66 kDa 
• Atom Count: 3,371 
• Modeled Residue Count: 386 
• Deposited Residue Count: 413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mandelate racemase/muconate lactonizing protein	A	413	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0  Gene Names: Dshi_2447 EC: 4.2.1.90
UniProt
Find proteins for A8LS88 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LS88  Go to UniProtKB:  A8LS88

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.304	α = 90
b = 137.304	β = 90
c = 115.216	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Kumaran, D., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2012-03-21
  Changes: Structure summary
• Version 1.2: 2014-04-02
  Changes: Other
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description