4QKO | pdb_00004qko

The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms

PDB DOI: https://doi.org/10.2210/pdb4QKO/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-07 Released: 2015-06-10
Deposition Author(s): Grinter, R., Josts, I., Roszak, A.W., Cogdell, C.J., Walker, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.215 (Depositor), 0.224 (DCC)
R-Value Work:
0.172 (Depositor), 0.182 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural Insights into pyocin S2

Grinter, R., Josts, I., McCaughey, L.C., Roszak, A.W., Walen, K.I., Kelly, S., Byron, O., Walker, D.

To be published.

Macromolecule Content

Total Structure Weight: 105.47 kDa
Atom Count: 7,820
Modeled Residue Count: 873
Deposited Residue Count: 916
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyocin-S2 immunity protein	A, C, E, G	95	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: imm2
UniProt
Find proteins for Q06579 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q06579 Go to UniProtKB: Q06579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06579
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyocin-S2	B, D, F, H	134	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: pys2 EC: 3.1
UniProt
Find proteins for Q06584 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q06584 Go to UniProtKB: Q06584
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain LA [auth G] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain NA [auth G] SDF format, chain OA [auth H] SDF format, chain P [auth C] SDF format, chain PA [auth H] SDF format, chain Q [auth C] SDF format, chain QA [auth H] SDF format, chain R [auth C] SDF format, chain RA [auth H] SDF format, chain S [auth D] SDF format, chain SA [auth H] SDF format, chain T [auth D] SDF format, chain TA [auth H] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth D] SDF format, chain MA [auth G] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth C] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth D] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain MA [auth G] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth H] mmCIF format, chain P [auth C] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain QA [auth H] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth D] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth D] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain MA [auth G]	AA [auth E] BA [auth E] CA [auth E] DA [auth F] EA [auth F] AA [auth E], BA [auth E], CA [auth E], DA [auth F], EA [auth F], FA [auth F], GA [auth F], HA [auth F], I [auth A], IA [auth F], J [auth A], K [auth A], KA [auth F], L [auth B], LA [auth G], M [auth B], MA [auth G], N [auth B], NA [auth G], OA [auth H], P [auth C], PA [auth H], Q [auth C], QA [auth H], R [auth C], RA [auth H], S [auth D], SA [auth H], T [auth D], TA [auth H], U [auth D], V [auth D], W [auth D], X [auth D], Z [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain NA [auth G] Focus chain OA [auth H] Focus chain P [auth C] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain QA [auth H] Focus chain R [auth C] Focus chain RA [auth H] Focus chain S [auth D] Focus chain SA [auth H] Focus chain T [auth D] Focus chain TA [auth H] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain NA [auth G] Focus chain OA [auth H] Focus chain P [auth C] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain QA [auth H] Focus chain R [auth C] Focus chain RA [auth H] Focus chain S [auth D] Focus chain SA [auth H] Focus chain T [auth D] Focus chain TA [auth H] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain JA [auth F] SDF format, chain O [auth B] SDF format, chain UA [auth H] SDF format, chain Y [auth D] MOL2 format, chain JA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain Y [auth D] mmCIF format, chain JA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain Y [auth D]	JA [auth F], O [auth B], UA [auth H], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain JA [auth F] Focus chain O [auth B] Focus chain UA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain JA [auth F] Focus chain O [auth B] Focus chain UA [auth H] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.215 (Depositor), 0.224 (DCC)
R-Value Work: 0.172 (Depositor), 0.182 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.39	α = 90
b = 114.42	β = 90
c = 120.22	γ = 90

Software Package:

Software Name	Purpose
EDNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description