7PDI | pdb_00007pdi

Crystal structure of the holo-acyl carrier protein (holo-AcpP) from Pseudomonas putida KT2440. Produced as an apo/holo mixture.

• PDB DOI: https://doi.org/10.2210/pdb7PDI/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-05 Released: 2021-08-18 
• Deposition Author(s): Venter, P., Sewell, B.T., Trindade, M., Mandyoli, L., van Zyl, L.
• Funding Organization(s): Global Challenges Research Fund, National Research Foundation in South Africa, Council of Scientific & Industrial Research (CSIR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the holo-acyl carrier protein (holo-AcpP) from Pseudomonas putida. Produced as an apo/holo mixture.

Venter, P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 9.34 kDa 
• Atom Count: 688 
• Modeled Residue Count: 82 
• Deposited Residue Count: 82 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	A	82	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: acpP, PP_1915
UniProt
Find proteins for Q88LL5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88LL5  Go to UniProtKB:  Q88LL5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4HH	A	L-PEPTIDE LINKING	C14 H28 N3 O9 P S		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.220 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.492	α = 90
b = 56.973	β = 90
c = 61.937	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Venter, P., Sewell, B.T., Trindade, M., Mandyoli, L., van Zyl, L.

---

Funding Organization	Location	Grant Number
Global Challenges Research Fund	United Kingdom	GCRF-START ST/R002754/1
National Research Foundation in South Africa	South Africa	110428
Council of Scientific & Industrial Research (CSIR)	South Africa	DSI-CSIR IBS

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description, Structure summary