4MTK | pdb_00004mtk

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

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
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

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.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VgrG1
A, B, C, D, E
A, B, C, D, E, F
643Pseudomonas aeruginosa PAO1Mutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I741
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TAM

Query on TAM


Download:Ideal Coordinates CCD File
CB [auth A],
CG [auth D]		TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth C]
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) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.275α = 90
b = 168.275β = 90
c = 652.849γ = 120
Software Package:
Software NamePurpose
RESOLVEmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
RESOLVEphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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