3MQT | pdb_00003mqt

Crystal structure of a mandelate racemase/muconate lactonizing enzyme from Shewanella pealeana

• PDB DOI: https://doi.org/10.2210/pdb3MQT/pdb

• Classification: ISOMERASE
• Organism(s): Shewanella pealeana ATCC 700345
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-28 Released: 2010-05-12 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal STRUCTURE OF A MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM SHEWANELLA PEALEANA

Agarwal, R., Burley, S.K., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1,068.04 kDa 
• Atom Count: 72,942 
• Modeled Residue Count: 9,063 
• Deposited Residue Count: 9,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	394	Shewanella pealeana ATCC 700345	Mutation(s): 0  Gene Names: Spea_3246
UniProt
Find proteins for A8H7M5 (Shewanella pealeana (strain ATCC 700345 / ANG-SQ1)) Explore A8H7M5  Go to UniProtKB:  A8H7M5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	AA [auth E], BA [auth F], CA [auth G], DA [auth H], EA [auth K], FA [auth L], GA [auth U], HA [auth V], IA [auth W], JA [auth X], Y [auth A], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.164	α = 98.47
b = 146.142	β = 96.8
c = 158.71	γ = 105.04

Software Package:

Software Name	Purpose
CBASS	data collection
CCP4	model building
MOLREP	phasing
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-05-12
  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: 2023-09-06
  Changes: Data collection, Database references, Refinement description