4S37

Crystal structure of R2 pyocin membrane-piercing spike

PDB DOI: https://doi.org/10.2210/pdb4S37/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-01-26 Released: 2016-01-27
Deposition Author(s): Browning, C.B., Leiman, P.G., Shneider, M.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.208
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of R2 pyocin membrane-piercing spike

Browning, C.B., Leiman, P.G., Shneider, M.M.

To be published.

Macromolecule Content

Total Structure Weight: 354.85 kDa
Atom Count: 26,421
Modelled Residue Count: 3,104
Deposited Residue Count: 3,330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage baseplate protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	185	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: VR2, gpV, D480_28305, JF43_02945, NCGM1900_0632, NCGM1984_0630
UniProt
Find proteins for Q9S581 (Pseudomonas aeruginosa) Explore Q9S581 Go to UniProtKB: Q9S581
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9S581
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain WA [auth H] MOL2 format, chain WA [auth H]	WA [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain WA [auth H] Interactions & Density Focus chain WA [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain XA [auth H] SDF format, chain AA [auth C] SDF format, chain AC [auth O] SDF format, chain BA [auth C] SDF format, chain BC [auth O] SDF format, chain CC [auth O] SDF format, chain DB [auth I] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain FC [auth P] SDF format, chain GB [auth J] SDF format, chain GC [auth R] SDF format, chain HB [auth J] SDF format, chain HC [auth R] SDF format, chain IB [auth J] SDF format, chain JA [auth E] SDF format, chain NA [auth F] SDF format, chain NB [auth K] SDF format, chain OA [auth F] SDF format, chain OB [auth K] SDF format, chain S [auth A] SDF format, chain SA [auth G] SDF format, chain SB [auth L] SDF format, chain TA [auth G] SDF format, chain TB [auth L] SDF format, chain V [auth B] SDF format, chain VB [auth M] SDF format, chain W [auth B] SDF format, chain WB [auth M] SDF format, chain X [auth B] SDF format, chain XB [auth M] SDF format, chain YA [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth H] SDF format, chain ZB [auth N] MOL2 format, chain XA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain AC [auth O] MOL2 format, chain BA [auth C] MOL2 format, chain BC [auth O] MOL2 format, chain CC [auth O] MOL2 format, chain DB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain FC [auth P] MOL2 format, chain GB [auth J] MOL2 format, chain GC [auth R] MOL2 format, chain HB [auth J] MOL2 format, chain HC [auth R] MOL2 format, chain IB [auth J] MOL2 format, chain JA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain NB [auth K] MOL2 format, chain OA [auth F] MOL2 format, chain OB [auth K] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain SB [auth L] MOL2 format, chain TA [auth G] MOL2 format, chain TB [auth L] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth M] MOL2 format, chain W [auth B] MOL2 format, chain WB [auth M] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth M] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain ZB [auth N]	AA [auth C] AC [auth O] BA [auth C] BC [auth O] CC [auth O] AA [auth C], AC [auth O], BA [auth C], BC [auth O], CC [auth O], DB [auth I], EA [auth D], FA [auth D], FC [auth P], GB [auth J], GC [auth R], HB [auth J], HC [auth R], IB [auth J], JA [auth E], NA [auth F], NB [auth K], OA [auth F], OB [auth K], S [auth A], SA [auth G], SB [auth L], TA [auth G], TB [auth L], V [auth B], VB [auth M], W [auth B], WB [auth M], X [auth B], XA [auth H], XB [auth M], YA [auth H], Z [auth C], ZA [auth H], ZB [auth N]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain AC [auth O] Focus chain BA [auth C] Focus chain BC [auth O] Focus chain CC [auth O] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain FC [auth P] Focus chain GB [auth J] Focus chain GC [auth R] Focus chain HB [auth J] Focus chain HC [auth R] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain OA [auth F] Focus chain OB [auth K] Focus chain S [auth A] Focus chain SA [auth G] Focus chain SB [auth L] Focus chain TA [auth G] Focus chain TB [auth L] Focus chain V [auth B] Focus chain VB [auth M] Focus chain W [auth B] Focus chain WB [auth M] Focus chain X [auth B] Focus chain XA [auth H] Focus chain XB [auth M] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Focus chain ZB [auth N] Interactions & Density Focus chain AA [auth C] Focus chain AC [auth O] Focus chain BA [auth C] Focus chain BC [auth O] Focus chain CC [auth O] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain FC [auth P] Focus chain GB [auth J] Focus chain GC [auth R] Focus chain HB [auth J] Focus chain HC [auth R] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain OA [auth F] Focus chain OB [auth K] Focus chain S [auth A] Focus chain SA [auth G] Focus chain SB [auth L] Focus chain TA [auth G] Focus chain TB [auth L] Focus chain V [auth B] Focus chain VB [auth M] Focus chain W [auth B] Focus chain WB [auth M] Focus chain X [auth B] Focus chain XA [auth H] Focus chain XB [auth M] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Focus chain ZB [auth N]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain MA [auth F] SDF format, chain DA [auth D] SDF format, chain MB [auth K] SDF format, chain RA [auth G] SDF format, chain RB [auth L] SDF format, chain U [auth B] SDF format, chain YB [auth N] MOL2 format, chain MA [auth F] MOL2 format, chain DA [auth D] MOL2 format, chain MB [auth K] MOL2 format, chain RA [auth G] MOL2 format, chain RB [auth L] MOL2 format, chain U [auth B] MOL2 format, chain YB [auth N]	DA [auth D] MA [auth F] MB [auth K] RA [auth G] RB [auth L] DA [auth D], MA [auth F], MB [auth K], RA [auth G], RB [auth L], U [auth B], YB [auth N]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain RA [auth G] Focus chain RB [auth L] Focus chain U [auth B] Focus chain YB [auth N] Interactions & Density Focus chain DA [auth D] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain RA [auth G] Focus chain RB [auth L] Focus chain U [auth B] Focus chain YB [auth N]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain DC [auth O] SDF format, chain GA [auth D] SDF format, chain JB [auth J] SDF format, chain PA [auth F] SDF format, chain Y [auth B] MOL2 format, chain AB [auth H] MOL2 format, chain DC [auth O] MOL2 format, chain GA [auth D] MOL2 format, chain JB [auth J] MOL2 format, chain PA [auth F] MOL2 format, chain Y [auth B]	AB [auth H] DC [auth O] GA [auth D] JB [auth J] PA [auth F] AB [auth H], DC [auth O], GA [auth D], JB [auth J], PA [auth F], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain DC [auth O] Focus chain GA [auth D] Focus chain JB [auth J] Focus chain PA [auth F] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth H] Focus chain DC [auth O] Focus chain GA [auth D] Focus chain JB [auth J] Focus chain PA [auth F] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EC [auth O] SDF format, chain UA [auth G] SDF format, chain BB [auth H] SDF format, chain CA [auth C] SDF format, chain CB [auth H] SDF format, chain EB [auth I] SDF format, chain FB [auth I] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain KA [auth E] SDF format, chain KB [auth J] SDF format, chain LA [auth E] SDF format, chain LB [auth J] SDF format, chain PB [auth K] SDF format, chain QA [auth F] SDF format, chain QB [auth K] SDF format, chain T [auth A] SDF format, chain UB [auth L] SDF format, chain VA [auth G] MOL2 format, chain EC [auth O] MOL2 format, chain UA [auth G] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain EB [auth I] MOL2 format, chain FB [auth I] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth J] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth J] MOL2 format, chain PB [auth K] MOL2 format, chain QA [auth F] MOL2 format, chain QB [auth K] MOL2 format, chain T [auth A] MOL2 format, chain UB [auth L] MOL2 format, chain VA [auth G]	BB [auth H] CA [auth C] CB [auth H] EB [auth I] EC [auth O] BB [auth H], CA [auth C], CB [auth H], EB [auth I], EC [auth O], FB [auth I], HA [auth D], IA [auth D], KA [auth E], KB [auth J], LA [auth E], LB [auth J], PB [auth K], QA [auth F], QB [auth K], T [auth A], UA [auth G], UB [auth L], VA [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain EB [auth I] Focus chain EC [auth O] Focus chain FB [auth I] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain KB [auth J] Focus chain LA [auth E] Focus chain LB [auth J] Focus chain PB [auth K] Focus chain QA [auth F] Focus chain QB [auth K] Focus chain T [auth A] Focus chain UA [auth G] Focus chain UB [auth L] Focus chain VA [auth G] Interactions & Density Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain EB [auth I] Focus chain EC [auth O] Focus chain FB [auth I] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain KB [auth J] Focus chain LA [auth E] Focus chain LB [auth J] Focus chain PB [auth K] Focus chain QA [auth F] Focus chain QB [auth K] Focus chain T [auth A] Focus chain UA [auth G] Focus chain UB [auth L] Focus chain VA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.208
R-Value Work: 0.163
R-Value Observed: 0.165
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.945	α = 90
b = 137.471	β = 106.56
c = 164.759	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Browning, C.B.

Leiman, P.G.

Shneider, M.M.

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2017-11-22
Changes: Advisory, Refinement description
Version 1.2: 2024-02-28
Changes: Advisory, Data collection, Database references, Derived calculations