1T8K | pdb_00001t8k

Crystal Structure of apo acyl carrier protein from E. coli

• PDB DOI: https://doi.org/10.2210/pdb1T8K/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-13 Released: 2004-09-07 
• Deposition Author(s): Qiu, X., Janson, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.150 (Depositor) 
• R-Value Work: 
  0.133 (Depositor) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions.

Qiu, X., Janson, C.A.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1545-1554

• PubMed: 15333924 
• DOI: https://doi.org/10.1107/S0907444904015422
• Primary Citation Related Structures: 
  1T8K


• PubMed Abstract: 
  

  A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 A resolution with MAD phasing using anomalous signals from the co-crystallized Zn(2+) ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn(2+) and solving the structures using anomalous signals.

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Organizational Affiliation: 
• GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.58 kDa 
• Atom Count: 750 
• Modeled Residue Count: 77 
• Deposited Residue Count: 77 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	A	77	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.150 (Depositor) 
• R-Value Work:  0.133 (Depositor) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.51	α = 90
b = 41.26	β = 90
c = 62.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-07 
Deposition Author(s): Qiu, X., Janson, C.A.

Revision History  

• Version 1.0: 2004-09-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations