6U83 | pdb_00006u83

OmpA-like domain of FopA1 from Francisella tularensis subsp. tularensis SCHU S4

PDB DOI: https://doi.org/10.2210/pdb6U83/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-04 Released: 2019-09-18
Deposition Author(s): Michalska, K., Skarina, T., Stogios, P.J., Di Leo, R., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

OmpA-like domain of FopA1 from Francisella tularensis subsp. tularensis SCHU S4

Michalska, K., Skarina, T., Stogios, P.J., Di Leo, R., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 19.31 kDa
Atom Count: 1,222
Modeled Residue Count: 154
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane associated protein	A	174	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: fopA1, FTT_0583
UniProt
Find proteins for Q5NH85 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NH85 Go to UniProtKB: Q5NH85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NH85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DAL (Subject of Investigation/LOI) Query on DAL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	D-ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-UWTATZPHSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.209 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.788	α = 90
b = 134.971	β = 90
c = 31.206	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary