3LVU

Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi

• PDB DOI: https://doi.org/10.2210/pdb3LVU/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Ruegeria pomeroyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-22 Released: 2010-03-02 
• Deposition Author(s): Chang, C., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi

Chang, C., Chhor, G., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.26 kDa 
• Atom Count: 9,093 
• Modelled Residue Count: 1,031 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, periplasmic substrate-binding protein	A, B, C, D	258	Ruegeria pomeroyi	Mutation(s): 0  Gene Names: SPO2066
UniProt
Find proteins for Q5LRQ9 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LRQ9  Go to UniProtKB:  Q5LRQ9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	P [auth B], Q [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N
IOD	AA [auth D], BA [auth D], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	H [auth A], O [auth B], W [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	M [auth B], N [auth B], R [auth B], S [auth B], X [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.384	α = 82.63
b = 75.517	β = 80.29
c = 78.477	γ = 77.42

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Chang, C., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary