3TDQ | pdb_00003tdq

Crystal structure of a fimbrial biogenesis protein PilY2 (PilY2_PA4555) from Pseudomonas aeruginosa PAO1 at 2.10 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3TDQ/pdb

• Classification: CELL ADHESION
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-11 Released: 2011-08-31 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of a fimbrial biogenesis protein PilY2 (PA4555) from Pseudomonas aeruginosa PAO1 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 22.91 kDa 
• Atom Count: 1,418 
• Modeled Residue Count: 163 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PilY2 protein	A, B	98	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: pilY2, PA4555
UniProt
Find proteins for Q51537 (Pseudomonas aeruginosa) Explore Q51537  Go to UniProtKB:  Q51537

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TDQ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.156	α = 90
b = 53.582	β = 90
c = 76.667	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary