2PG3 | pdb_00002pg3

Crystal structure of a Queuosine biosynthesis protein queC (ECA1155) from Erwinia carotovora subsp. atroseptica SCRI1043 at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PG3/pdb

• Classification: HYDROLASE
• Organism(s): Pectobacterium atrosepticum SCRI1043
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-06 Released: 2007-04-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of hypothetical protein (YP_049261.1) from Erwinia carotovora subsp. atroseptica SCRI1043 at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 25.65 kDa 
• Atom Count: 1,700 
• Modeled Residue Count: 221 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuosine biosynthesis protein queC	A	232	Pectobacterium atrosepticum SCRI1043	Mutation(s): 3  Gene Names: YP_049261.1, queC, ECA1155 EC: 3.5 (PDB Primary Data), 6.3.4.20 (UniProt)
UniProt
Find proteins for Q6D820 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D820  Go to UniProtKB:  Q6D820

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.40 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32PG3

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.154	α = 90
b = 78.154	β = 90
c = 77.755	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2014-12-24
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2017-10-25
  Changes: Author supporting evidence
• Version 1.6: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.7: 2024-11-20
  Changes: Data collection, Structure summary