4MTK | pdb_00004mtk

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

• PDB DOI: https://doi.org/10.2210/pdb4MTK/pdb

• Classification: TOXIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-19 Released: 2014-10-01 
• Deposition Author(s): Sycheva, L.V., Shneider, M.M., Leiman, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

The conserved architecture of the T6SS central spike complex

Sycheva, L.V., Shneider, M.M., Basler, M., Ho, B.T., Mekalanos, J.J., Leiman, P.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 457.51 kDa 
• Atom Count: 31,170 
• Modeled Residue Count: 3,762 
• Deposited Residue Count: 3,858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VgrG1	A, B, C, D, E, F	643	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA0091, vgrG1
UniProt
Find proteins for Q9I741 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I741  Go to UniProtKB:  Q9I741

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAM	CB [auth A], CG [auth D]	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N
SO4	AA [auth A], AB [auth A], AC [auth B], AD [auth B], AE [auth C], AF [auth D], AG [auth D], AH [auth E], AI [auth F], AJ [auth F], BA [auth A], BB [auth A], BC [auth B], BD [auth B], BE [auth C], BF [auth D], BG [auth D], BH [auth E], BI [auth F], BJ [auth F], CA [auth A], CC [auth B], CD [auth C], CE [auth C], CF [auth D], CH [auth E], CI [auth F], CJ [auth F], DA [auth A], DB [auth A], DC [auth B], DD [auth C], DE [auth C], DF [auth D], DG [auth D], DH [auth E], DI [auth F], DJ [auth F], EA [auth A], EB [auth B], EC [auth B], ED [auth C], EE [auth C], EF [auth D], EG [auth E], EH [auth E], EI [auth F], FA [auth A], FB [auth B], FC [auth B], FD [auth C], FE [auth C], FF [auth D], FG [auth E], FH [auth E], FI [auth F], G [auth A], GA [auth A], GB [auth B], GC [auth B], GD [auth C], GE [auth C], GF [auth D], GG [auth E], GH [auth E], GI [auth F], H [auth A], HA [auth A], HB [auth B], HC [auth B], HD [auth C], HE [auth C], HF [auth D], HG [auth E], HH [auth E], HI [auth F], I [auth A], IA [auth A], IB [auth B], IC [auth B], ID [auth C], IE [auth C], IF [auth D], IG [auth E], IH [auth E], II [auth F], J [auth A], JA [auth A], JB [auth B], JC [auth B], JD [auth C], JE [auth C], JF [auth D], JG [auth E], JH [auth E], JI [auth F], K [auth A], KA [auth A], KB [auth B], KC [auth B], KD [auth C], KE [auth C], KF [auth D], KG [auth E], KH [auth E], KI [auth F], L [auth A], LA [auth A], LB [auth B], LC [auth B], LD [auth C], LE [auth C], LF [auth D], LG [auth E], LH [auth E], LI [auth F], M [auth A], MA [auth A], MB [auth B], MC [auth B], MD [auth C], ME [auth C], MF [auth D], MG [auth E], MH [auth F], MI [auth F], N [auth A], NA [auth A], NB [auth B], NC [auth B], ND [auth C], NE [auth C], NF [auth D], NG [auth E], NH [auth F], NI [auth F], O [auth A], OA [auth A], OB [auth B], OC [auth B], OD [auth C], OE [auth C], OF [auth D], OG [auth E], OH [auth F], OI [auth F], P [auth A], PA [auth A], PB [auth B], PC [auth B], PD [auth C], PE [auth C], PF [auth D], PG [auth E], PH [auth F], PI [auth F], Q [auth A], QA [auth A], QB [auth B], QC [auth B], QD [auth C], QE [auth C], QF [auth D], QG [auth E], QH [auth F], QI [auth F], R [auth A], RA [auth A], RB [auth B], RC [auth B], RD [auth C], RE [auth C], RF [auth D], RG [auth E], RH [auth F], RI [auth F], S [auth A], SA [auth A], SB [auth B], SC [auth B], SD [auth C], SE [auth C], SF [auth D], SG [auth E], SH [auth F], SI [auth F], T [auth A], TA [auth A], TB [auth B], TC [auth B], TD [auth C], TE [auth C], TF [auth D], TG [auth E], TH [auth F], TI [auth F], U [auth A], UA [auth A], UB [auth B], UC [auth B], UD [auth C], UE [auth D], UF [auth D], UG [auth E], UH [auth F], UI [auth F], V [auth A], VA [auth A], VB [auth B], VC [auth B], VD [auth C], VE [auth D], VF [auth D], VG [auth E], VH [auth F], VI [auth F], W [auth A], WA [auth A], WB [auth B], WC [auth B], WD [auth C], WE [auth D], WF [auth D], WG [auth E], WH [auth F], WI [auth F], X [auth A], XA [auth A], XB [auth B], XC [auth B], XD [auth C], XE [auth D], XF [auth D], XG [auth E], XH [auth F], XI [auth F], Y [auth A], YA [auth A], YB [auth B], YC [auth B], YD [auth C], YE [auth D], YF [auth D], YG [auth E], YH [auth F], YI [auth F], Z [auth A], ZA [auth A], ZB [auth B], ZC [auth B], ZD [auth C], ZE [auth D], ZF [auth D], ZG [auth E], ZH [auth F], ZI [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/235

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.275	α = 90
b = 168.275	β = 90
c = 652.849	γ = 120

Software Package:

Software Name	Purpose
RESOLVE	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Sycheva, L.V., Shneider, M.M., Leiman, P.G.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description