3FG9 | pdb_00003fg9

The crystal structure of an universal stress protein UspA family protein from Lactobacillus plantarum WCFS1

PDB DOI: https://doi.org/10.2210/pdb3FG9/pdb

Classification: structural genomics, unknown function
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-12-05 Released: 2008-12-23
Deposition Author(s): Tan, K., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.212 (Depositor), 0.209 (DCC)
R-Value Work:
0.177 (Depositor), 0.175 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of an universal stress protein UspA family protein from Lactobacillus plantarum WCFS1

Tan, K., Li, H., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 105.58 kDa
Atom Count: 8,212
Modeled Residue Count: 893
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein of universal stress protein UspA family	A, B, C, D, E A, B, C, D, E, F	156	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: Lactobacillus plantarum, lp_3663
UniProt
Find proteins for F9ULL0 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9ULL0 Go to UniProtKB: F9ULL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9ULL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain Q [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D]	H [auth A] I [auth A] K [auth B] M [auth C] N [auth C] H [auth A], I [auth A], K [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F]	G [auth A] J [auth B] L [auth C] P [auth D] S [auth E] G [auth A], J [auth B], L [auth C], P [auth D], S [auth E], T [auth E], U [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.212 (Depositor), 0.209 (DCC)
R-Value Work: 0.177 (Depositor), 0.175 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.355	α = 90
b = 118.949	β = 90
c = 191.974	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-12-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary