3H35 | pdb_00003h35

Structure of the uncharacterized protein ABO_0056 from the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2.

• PDB DOI: https://doi.org/10.2210/pdb3H35/pdb

• Classification: structural genomics, unknown function
• Organism(s): Alcanivorax borkumensis SK2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-15 Released: 2009-05-12 
• Deposition Author(s): Cuff, M.E., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Structure of the uncharacterized protein ABO_0056 from the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2.

Cuff, M.E., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.11 kDa 
• Atom Count: 3,670 
• Modeled Residue Count: 425 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein ABO_0056	A, B, C	185	Alcanivorax borkumensis SK2	Mutation(s): 0  Gene Names: ABO_0056
UniProt
Find proteins for Q0VTF8 (Alcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2)) Explore Q0VTF8  Go to UniProtKB:  Q0VTF8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	E [auth C]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.967	α = 90
b = 82.967	β = 90
c = 131.485	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: 2009-05-12 
Deposition Author(s): Cuff, M.E., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary