4E4U | pdb_00004e4u

Crystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200780) from Burkholderia SAR-1

• PDB DOI: https://doi.org/10.2210/pdb4E4U/pdb

• Classification: ISOMERASE
• Organism(s): unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-13 Released: 2012-04-18 
• Deposition Author(s): Kumar, P.R., Bonanno, J., Chowdhury, S., Foti, R., Gizzi, A., Hammonds, J., Hillerich, B., Matikainen, B., Seidel, R., Toro, R., Zencheck, W., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.146 (Depositor), 0.142 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

Crystal structure of a putative MR/ML enzyme from Burkholderia SAR-1

Kumar, P.R., Bonanno, J., Chowdhury, S., Foti, R., Gizzi, A., Hammonds, J., Hillerich, B., Matikainen, B., Seidel, R., Toro, R., Zencheck, W., Almo, S.C.

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: 45.8 kDa 
• Atom Count: 3,646 
• Modeled Residue Count: 403 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandalate racemase/muconate lactonizing enzyme	A	412	unidentified	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTU	B [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-ZXZARUISSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.146 (Depositor), 0.142 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.835	α = 90
b = 118.835	β = 90
c = 120.839	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Kumar, P.R., Bonanno, J., Chowdhury, S., Foti, R., Gizzi, A., Hammonds, J., Hillerich, B., Matikainen, B., Seidel, R., Toro, R., Zencheck, W., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations