3GKB | pdb_00003gkb

Crystal structure of a putative enoyl-CoA hydratase from Streptomyces avermitilis

• PDB DOI: https://doi.org/10.2210/pdb3GKB/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptomyces avermitilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-10 Released: 2009-03-24 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Wasserman, 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: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of a putative enoyl-CoA hydratase from Streptomyces avermitilis

Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 91.89 kDa 
• Atom Count: 6,884 
• Modeled Residue Count: 830 
• Deposited Residue Count: 861 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative enoyl-CoA hydratase	A, B, C	287	Streptomyces avermitilis	Mutation(s): 0  Gene Names: echA1, SAV492, SAV_492
UniProt
Find proteins for Q82QL3 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82QL3  Go to UniProtKB:  Q82QL3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth B], F [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.461	α = 90
b = 87.502	β = 90
c = 154.447	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references