1NL7 | pdb_00001nl7

Z. ramigera biosynthetic thiolase, acetylated enzyme complexed with CoA at pH 9.5

• PDB DOI: https://doi.org/10.2210/pdb1NL7/pdb

• Classification: TRANSFERASE
• Organism(s): Zoogloea ramigera
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-06 Released: 2004-04-06 
• Deposition Author(s): Kursula, P., Wierenga, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of Z. ramigera biosynthetic thiolase

Kursula, P., Wierenga, R.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 164.25 kDa 
• Atom Count: 12,691 
• Modeled Residue Count: 1,560 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A, B, C, D	392	Zoogloea ramigera	Mutation(s): 1  EC: 2.3.1.9
UniProt
Find proteins for P07097 (Shinella zoogloeoides) Explore P07097  Go to UniProtKB:  P07097

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	G [auth A], J [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SO4	E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY	A, B, C, D	L-PEPTIDE LINKING	C5 H9 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.374	α = 90
b = 79.059	β = 92.58
c = 148.881	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-06 
Deposition Author(s): Kursula, P., Wierenga, R.K.

Revision History  

• Version 1.0: 2004-04-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary