1K77

Crystal Structure of EC1530, a Putative Oxygenase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1K77/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-10-18 Released: 2002-03-13 
• Deposition Author(s): Kim, Y., Skarina, T., Beasley, S., Laskowski, R., Arrowsmith, C.H., Joachimiak, A., Edwards, A.M., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.

Kim, Y., Skarina, T., Beasley, S., Laskowski, R., Arrowsmith, C.H., Joachimiak, A., Edwards, A.M., Savchenko, A.

(2002) Proteins 48: 427-430

• PubMed: 12112708 
• DOI: https://doi.org/10.1002/prot.10160
• Primary Citation of Related Structures:  
  1K77

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Organizational Affiliation: 

Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.86 kDa 
• Atom Count: 2,438 
• Modelled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ygbM	A	260	Escherichia coli	Mutation(s): 4
UniProt
Find proteins for Q46891 (Escherichia coli (strain K12)) Explore Q46891  Go to UniProtKB:  Q46891

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.63 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.907	α = 90
b = 74.368	β = 98.81
c = 39.376	γ = 90

Software Package:

Software Name	Purpose
d*treck/HKL2000	data collection
HKL-2000	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-13 
Deposition Author(s): Kim, Y., Skarina, T., Beasley, S., Laskowski, R., Arrowsmith, C.H., Joachimiak, A., Edwards, A.M., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2002-03-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance