4OLQ | pdb_00004olq

Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium

• PDB DOI: https://doi.org/10.2210/pdb4OLQ/pdb

• Classification: LYASE
• Organism(s): Hyphomonas neptunium ATCC 15444
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-24 Released: 2014-03-12 
• Deposition Author(s): Szlachta, K., Cooper, D.R., Chapman, H.C., Cymborowski, M.T., 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: 2.70 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium

Szlachta, K., Cooper, D.R., Chapman, H.C., Cymborowski, M.T., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W.

To be published.

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 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: 182.59 kDa 
• Atom Count: 11,585 
• Modeled Residue Count: 1,597 
• Deposited Residue Count: 1,692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A, B, C, D, E, F	282	Hyphomonas neptunium ATCC 15444	Mutation(s): 0  Gene Names: HNE_1107 EC: 4.2.1.17
UniProt
Find proteins for Q0C365 (Hyphomonas neptunium (strain ATCC 15444)) Explore Q0C365  Go to UniProtKB:  Q0C365

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	J [auth C], R [auth F]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	K [auth C], S [auth F]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MLT	H [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
PEG	P [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
UNL	G [auth A], I [auth B], L [auth C], M [auth D], N [auth D], O [auth D], Q [auth E], T [auth F]	Unknown ligand 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: 2.70 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3MS3K

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.595	α = 90
b = 122.39	β = 90
c = 210.232	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Szlachta, K., Cooper, D.R., Chapman, H.C., Cymborowski, M.T., 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: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  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