Biological Assembly 1

Protein Symmetry: Cyclic - C14 (View in 3D)

Protein Stoichiometry: Hetero 42-mer - A14B14C14

Macromolecule Content

• Unique protein chains: 3

3JQO

Crystal structure of the outer membrane complex of a type IV secretion system

• DOI: 10.2210/pdb3jqo/pdb

• Classification: TRANSPORT PROTEIN
• Deposited: 2009-09-07 Released: 2009-12-01
• Deposition author(s): Chandran, V., Fronzes, R., Duquerroy, S., Cronin, N., Navaza, J., Waksman, G.
• Organism: Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): 1

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.259
• R-Value Work: 0.227

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: TRANSPORT PROTEIN

Total Structure Weight: 606128.13

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Outer Membrane Proteins

Protein Name: Type IV outer membrane secretion complex

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
LDA	J	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N	Poseview Image of LDA in 3JQO Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
MPD	D, h, k	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N	Poseview Image of MPD in 3JQO Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, W, Y, Z, b, c, e, f, h, i, k, l, n, o	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.259
• R-Value Work: 0.227
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 202.40	α = 90.00
b = 211.63	β = 90.00
c = 203.44	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2009-09-07
• Released Date: 2009-12-01
• Deposition author(s): Chandran, V., Fronzes, R., Duquerroy, S., Cronin, N., Navaza, J., Waksman, G.

Revision History

• 2011-07-13
  Type: Version format compliance
• 2014-02-12
  Type: Database references
• 2014-07-23
  Type: Other