6O6E

Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor

PDB DOI: https://doi.org/10.2210/pdb6O6E/pdb

Classification: Ligase/Transport protein
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-03-06 Released: 2020-04-08
Deposition Author(s): Corpuz, J.C., Podust, L.M.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.260
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Dynamic visualization of type II peptidyl carrier protein recognition in pyoluteorin biosynthesis.

Corpuz, J.C., Podust, L.M., Davis, T.D., Jaremko, M.J., Burkart, M.D.

(2020) RSC Chem Biol 1: 8-12

PubMed: 33305272 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/c9cb00015a
Primary Citation of Related Structures:
6O6E

PubMed Abstract:
Using a covalent chemical probe and X-ray crystallography coupled to nuclear magnetic resonance data, we elucidated the dynamic molecular basis of protein recognition between the carrier protein and adenylation domain in pyoluteorin biosynthesis. These findings reveal a unique binding mode, which contrasts previously solved carrier protein and partner protein interfaces.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.

Macromolecule Content

Total Structure Weight: 69.23 kDa
Atom Count: 4,552
Modelled Residue Count: 578
Deposited Residue Count: 609
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-proline--[L-prolyl-carrier protein] ligase	A [auth B]	513	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: pltF, PFL_2792 EC: 6.2.1.53
UniProt
Find proteins for Q4KCY5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KCY5 Go to UniProtKB: Q4KCY5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4KCY5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl carrier protein PltL	B [auth E]	96	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: pltL, PFL_2786
UniProt
Find proteins for Q4KCZ1 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KCZ1 Go to UniProtKB: Q4KCZ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4KCZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I5M (Subject of Investigation/LOI) Query on I5M Download Ideal Coordinates CCD File SDF format, chain S [auth E] MOL2 format, chain S [auth E]	S [auth E]	5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine C₂₇ H₄₄ N₉ O₁₁ P S₂ UUZQPBPCNSKBOR-LCZLERPASA-N		Interactions Focus chain S [auth E] Interactions & Density Focus chain S [auth E]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	Q [auth B], R [auth B]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain Q [auth B] Focus chain R [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.260
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.55	α = 90
b = 170.55	β = 90
c = 64.9	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Corpuz, J.C.

Podust, L.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	T32 GM008326
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01 GM095970

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2020-06-17
Changes: Database references
Version 2.0: 2020-07-22
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2020-11-11
Changes: Database references
Version 2.2: 2020-12-23
Changes: Database references
Version 3.0: 2022-07-20
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
Version 3.1: 2023-10-11
Changes: Data collection, Refinement description