3S3T | pdb_00003s3t

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 (Depositor), 0.220 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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.

Macromolecule Content

Total Structure Weight: 131.67 kDa
Atom Count: 10,263
Modeled Residue Count: 1,156
Deposited Residue Count: 1,168
Unique protein chains: 1

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 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
Sequence Annotations 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 O [auth C] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain R [auth D] SDF format, chain L [auth B] MOL2 format, chain AA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain R [auth D] MOL2 format, chain L [auth B] mmCIF format, chain AA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain R [auth D] mmCIF format, chain L [auth B]	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		Interactions Focus chain AA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	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		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth G] MOL2 format, chain DA [auth G] mmCIF format, chain DA [auth G]	DA [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Interactions & Density Focus chain DA [auth G]
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] mmCIF format, chain BA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF 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		Interactions Focus chain BA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [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, 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 (Depositor), 0.220 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33S3T

Space Group: P 1

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-06
Changes: Structure summary