3VC6 | pdb_00003vc6

Crystal structure of enolase Tbis_1083(TARGET EFI-502310) FROM Thermobispora bispora DSM 43833 complexed with magnesium and formate

• PDB DOI: https://doi.org/10.2210/pdb3VC6/pdb

• Classification: ISOMERASE
• Organism(s): Thermobispora bispora DSM 43833
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-03 Released: 2012-02-01 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of enolase Tbis_1083 FROM Thermobispora bispora DSM 43833

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., 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)

Macromolecule Content 

• Total Structure Weight: 48 kDa 
• Atom Count: 3,721 
• Modeled Residue Count: 420 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A	441	Thermobispora bispora DSM 43833	Mutation(s): 0  Gene Names: Tbis_1083 EC: 4.2.1.40
UniProt
Find proteins for D6Y7Y6 (Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / KCTC 9307 / NBRC 14880 / R51)) Explore D6Y7Y6  Go to UniProtKB:  D6Y7Y6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.115	α = 90
b = 78.115	β = 90
c = 166.039	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Structure summary
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description