9BLI | pdb_00009bli

Crystal structure of Actin capping protein in complex with a fragment of Legionella pneumophila RavB

• PDB DOI: https://doi.org/10.2210/pdb9BLI/pdb

• Classification: PROTEIN BINDING
• Organism(s): Gallus gallus, Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-30 Released: 2025-05-07 
• Deposition Author(s): Ye, J.S., Majumdar, A., Tomchick, D.R., Tagliabracci, V.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation, Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Bacterial ubiquitin ligase engineered for small molecule and protein target identification

Ye, J.S., Majumdar, A., Park, B., Black, M.H., Hsieh, T.-S., Osinski, A., Servage, K.A., Kulkarni, K., Naidoo, J., Alto, N.M., Stratton, M.M., Ready, J.M., Pawlowski, K., Tomchick, D.R., Tagliabracci, V.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 65.96 kDa 
• Atom Count: 4,594 
• Modeled Residue Count: 547 
• Deposited Residue Count: 576 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit alpha-1	A	286	Gallus gallus	Mutation(s): 0  Gene Names: CAPZA1
UniProt
Find proteins for P13127 (Gallus gallus) Explore P13127  Go to UniProtKB:  P13127

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit beta isoforms 1 and 2	B	248	Gallus gallus	Mutation(s): 0  Gene Names: CAPZB
UniProt
Find proteins for P14315 (Gallus gallus) Explore P14315  Go to UniProtKB:  P14315

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	C	42	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: lpg0030
UniProt
Find proteins for Q5ZZI0 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZI0  Go to UniProtKB:  Q5ZZI0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	D [auth A], E [auth A], F [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.502	α = 90
b = 55.322	β = 107.08
c = 77.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Ye, J.S., Majumdar, A., Tomchick, D.R., Tagliabracci, V.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM137419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	K99GM147532
Robert A. Welch Foundation	United States	I-1911
Robert A. Welch Foundation	United States	I-1704
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release