2P2S | pdb_00002p2s

Crystal structure of putative oxidoreductase (YP_050235.1) from Erwinia carotovora atroseptica SCRI1043 at 1.25 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2P2S/pdb

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


• Deposited: 2007-03-07 Released: 2007-03-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of putative oxidoreductase (YP_050235.1) from Erwinia carotovora atroseptica SCRI1043 at 1.25 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 (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 75.89 kDa 
• Atom Count: 6,386 
• Modeled Residue Count: 668 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B	336	Pectobacterium atrosepticum SCRI1043	Mutation(s): 5  Gene Names: YP_050235.1, ECA2140 EC: 1.1
UniProt
Find proteins for Q6D5A0 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D5A0  Go to UniProtKB:  Q6D5A0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32P2S

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.05	α = 90
b = 45.83	β = 116.4
c = 87.97	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary