3S3T

Universal stress protein UspA from Lactobacillus plantarum

PDB DOI: https://doi.org/10.2210/pdb3S3T/pdb

Classification: CHAPERONE
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-18 Released: 2011-06-08
Deposition Author(s): Osipiuk, J., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.221
R-Value Work: 0.168
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Universal stress protein UspA from Lactobacillus plantarum.

Osipiuk, J., Li, H., Cobb, G., Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding protein, universal stress protein UspA family	A, B, C, D, E, F, G, H A, B, C, D, E, F, G, H	146	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: lp_1163
UniProt
Find proteins for F9UMW3 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UMW3 Go to UniProtKB: F9UMW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9UMW3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F]	AA [auth G], EA [auth H], I [auth A], L [auth B], O [auth C], AA [auth G], EA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F]	CA [auth G], GA [auth H], K [auth A], N [auth B], Q [auth C], CA [auth G], GA [auth H], K [auth A], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth G] MOL2 format, chain DA [auth G]	DA [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain FA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F]	BA [auth G], FA [auth H], J [auth A], M [auth B], P [auth C], BA [auth G], FA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.221
R-Value Work: 0.168
R-Value Observed: 0.171
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M33S3T

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.015	α = 102.13
b = 56.187	β = 100.53
c = 109.144	γ = 90.36

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing