4NEK | pdb_00004nek

Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1

• PDB DOI: https://doi.org/10.2210/pdb4NEK/pdb

• Classification: ISOMERASE
• Organism(s): Paramagnetospirillum magneticum AMB-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-29 Released: 2013-11-27 
• Deposition Author(s): Tkaczuk, K.L., Cooper, D.R., Geffken, K., Chapman, H.C., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.207 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1

Tkaczuk, K.L., Cooper, D.R., Geffken, K., Chapman, H.C., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 163.65 kDa 
• Atom Count: 11,590 
• Modeled Residue Count: 1,508 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/carnithine racemase	A, B, C, D, E, F	252	Paramagnetospirillum magneticum AMB-1	Mutation(s): 0  Gene Names: amb4133
UniProt
Find proteins for Q2VZN8 (Paramagnetospirillum magneticum (strain ATCC 700264 / AMB-1)) Explore Q2VZN8  Go to UniProtKB:  Q2VZN8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A], H [auth B], I [auth D], J [auth D], K [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.207 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3BC7G

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.285	α = 90
b = 156.683	β = 113.81
c = 79.297	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Tkaczuk, K.L., Cooper, D.R., Geffken, K., Chapman, H.C., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary