3U24 | pdb_00003u24

The structure of a putative lipoprotein of unknown function from Shewanella oneidensis.

• PDB DOI: https://doi.org/10.2210/pdb3U24/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-30 Released: 2012-05-09 
• Deposition Author(s): Cuff, M.E., Hatzos-Skintges, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.200 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

The structure of a putative lipoprotein of unknown function from Shewanella oneidensis.

Cuff, M.E., Hatzos-Skintges, C., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.9 kDa 
• Atom Count: 4,888 
• Modeled Residue Count: 546 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Lipoprotein	A	572	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: SO_2570
UniProt
Find proteins for Q8EE20 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EE20  Go to UniProtKB:  Q8EE20

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	W [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	P [auth A], S [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	M [auth A], N [auth A], O [auth A], Q [auth A], U [auth A], Z [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	R [auth A], T [auth A], V [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.200 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.427	α = 90
b = 96.427	β = 90
c = 133.947	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Cuff, M.E., Hatzos-Skintges, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary