4DDF | pdb_00004ddf

Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group P4

PDB DOI: https://doi.org/10.2210/pdb4DDF/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Salmonella enterica
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-01-18 Released: 2012-06-06
Deposition Author(s): Sawaya, M.R., King, N.P., Sheffler, W., Baker, D., Yeates, T.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.221 (Depositor), 0.243 (DCC)
R-Value Work:
0.183 (Depositor), 0.201 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Computational design of self-assembling protein nanomaterials with atomic level accuracy.

King, N.P., Sheffler, W., Sawaya, M.R., Vollmar, B.S., Sumida, J.P., Andre, I., Gonen, T., Yeates, T.O., Baker, D.

(2012) Science 336: 1171-1174

PubMed: 22654060 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1219364
Primary Citation Related Structures:
3VCD, 4DCL, 4DDF, 4EGG

PubMed Abstract:
We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.

Organizational Affiliation

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content

Total Structure Weight: 241.15 kDa
Atom Count: 15,798
Modeled Residue Count: 2,196
Deposited Residue Count: 2,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propanediol utilization polyhedral body protein PduT	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	192	Salmonella enterica	Mutation(s): 10 Gene Names: PduT
UniProt
Find proteins for Q9XDM8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q9XDM8 Go to UniProtKB: Q9XDM8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9XDM8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain IA [auth L] SDF format, chain GA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], R [auth C], S [auth C], U [auth D], V [auth E], Y [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain Y [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain W [auth E] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain JA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain DA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], Q [auth B], T [auth C], W [auth E], X [auth F], Z [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.221 (Depositor), 0.243 (DCC)
R-Value Work: 0.183 (Depositor), 0.201 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.46	α = 90
b = 169.46	β = 90
c = 119.93	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XSCALE	data scaling
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2012-06-13
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations