6IJK | pdb_00006ijk

Enoyl-CoA hydratase/isomerase family protein from Cupriavidus necator H16

• PDB DOI: https://doi.org/10.2210/pdb6IJK/pdb

• Classification: LYASE
• Organism(s): Cupriavidus necator H16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-10 Released: 2019-08-21 
• Deposition Author(s): Seo, H., Kim, K.-J.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel type isomerase of enoyl-CoA hydratase/isomerase family protein from Cupriavidus necator H16

Seo, H., Kim, K.-J.

(2019) Biotechnol Bioprocess Eng 24: 155-162

• DOI: https://doi.org/10.1007/s12257-018-0393-3

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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)

Macromolecule Content 

• Total Structure Weight: 64.72 kDa 
• Atom Count: 4,127 
• Modeled Residue Count: 538 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase	A, B	299	Cupriavidus necator H16	Mutation(s): 0  Gene Names: H16_B0756 EC: 4.2.1.17
UniProt
Find proteins for Q0K371 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0K371  Go to UniProtKB:  Q0K371

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.941	α = 90
b = 132.941	β = 90
c = 44.164	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Seo, H., Kim, K.-J.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016M3D3A1A01913269
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M1A2A2087631
National Research Foundation (Korea)	Korea, Republic Of	NRF-2018H1A2A1061751

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-09-04
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description