3G27 | pdb_00003g27

Structure of a putative bacteriophage protein from Escherichia coli str. K-12 substr. MG1655

• PDB DOI: https://doi.org/10.2210/pdb3G27/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-30 Released: 2009-03-24 
• Deposition Author(s): Cuff, M.E., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Structure of a putative bacteriophage protein from Escherichia coli str. K-12 substr. MG1655

Cuff, M.E., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.63 kDa 
• Atom Count: 658 
• Modeled Residue Count: 81 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
82 prophage-derived uncharacterized protein ybcO	A	96	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0549, JW0537, ybcO EC: 3.1
UniProt
Find proteins for P68661 (Escherichia coli (strain K12)) Explore P68661  Go to UniProtKB:  P68661

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [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: 2.10 Å
• R-Value Free:  0.249 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.311	α = 90
b = 71.311	β = 90
c = 32.333	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
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
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Cuff, M.E., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary