3T8Q | pdb_00003t8q

Crystal structure of mandelate racemase/muconate lactonizing enzyme family protein from Hoeflea phototrophica

• PDB DOI: https://doi.org/10.2210/pdb3T8Q/pdb

• Classification: ISOMERASE
• Organism(s): Hoeflea phototrophica DFL-43
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-08-17 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mandelate racemase/muconate lactonizing enzyme family protein from Hoeflea phototrophica

Agarwal, R., Almo, S.C., Swaminathan, S.

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: 82.98 kDa 
• Atom Count: 6,408 
• Modeled Residue Count: 736 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme family protein	A, B	370	Hoeflea phototrophica DFL-43	Mutation(s): 0  Gene Names: HPDFL43_14512
UniProt
Find proteins for A9D2J3 (Hoeflea phototrophica (strain DSM 17068 / NCIMB 14078 / DFL-43)) Explore A9D2J3  Go to UniProtKB:  A9D2J3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	D [auth A], F [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.557	α = 90
b = 189.461	β = 90
c = 57.995	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description