3ISA | pdb_00003isa

CRYSTAL STRUCTURE OF putative enoyl-CoA hydratase/isomerase FROM Bordetella parapertussis

• PDB DOI: https://doi.org/10.2210/pdb3ISA/pdb

• Classification: HYDROLASE
• Organism(s): Bordetella parapertussis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-25 Released: 2009-09-01 
• Deposition Author(s): Patskovsky, Y., Malashkevich, V., Toro, R., Foti, R., Dickey, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

CRYSTAL STRUCTURE OF enoyl-CoA hydratase FROM Bordetella parapertussis

Patskovsky, Y., Malashkevich, V., Toro, R., Foti, R., Dickey, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 168.49 kDa 
• Atom Count: 13,353 
• Modeled Residue Count: 1,441 
• Deposited Residue Count: 1,524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative enoyl-CoA hydratase/isomerase	A, B, C, D, E, F	254	Bordetella parapertussis	Mutation(s): 0  Gene Names: BPP4107
UniProt
Find proteins for Q7W3D6 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W3D6  Go to UniProtKB:  Q7W3D6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AB [auth E], GA [auth C], GB [auth F], HA [auth C], IB [auth F], N [auth A], NA [auth D], P [auth A], QA [auth D], X [auth B], Y [auth B], Z [auth B], ZA [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	AA [auth C], BA [auth C], BB [auth E], CA [auth C], CB [auth E], DA [auth C], DB [auth F], EA [auth C], EB [auth F], FA [auth C], FB [auth F], G [auth A], H [auth A], HB [auth F], I [auth A], IA [auth D], J [auth A], JA [auth D], JB [auth F], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], O [auth A], OA [auth D], PA [auth D], Q [auth B], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], XA [auth E], YA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.837	α = 90
b = 120.825	β = 110.37
c = 78.577	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Patskovsky, Y., Malashkevich, V., Toro, R., Foti, R., Dickey, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references